Right or wrong? How feedback content and source influence children's mathematics performance and persistence

The current study examined how different features of corrective feedback influenced children's performance and motivational outcomes on a mathematics task. Elementary school-aged children from the United States (N = 130; Mage = 7.61 years; 35% female; 60% White) participated in a Zoom session with a trained researcher. During the learning activity, children solved a series of mathematical equivalence problems and were assigned to different feedback conditions that varied in feedback content (correct answer alone vs. correct answer with verification) and feedback source (computer alone vs. computer with person). In terms of content, feedback with verification cues led to decreased persistence, decreased strategy variability, and higher reliance on entrenched strategies relative to feedback that contained the correct answer alone. In terms of source, feedback from the computer alone enhanced children's accuracy; however, the most resilient children received feedback from the computer and a person. Findings are discussed in light of existing feedback theories.

Expecting the Unexpected: Infants Use Others' Surprise to Revise Their Own Expectations

Human infants show systematic responses to events that violate their expectations. Can they also revise these expectations based on others' expressions of surprise? Here we ask whether infants (N = 156, mean = 15.2 months, range: 12.0-18.0 months) can use an experimenter's expression of surprise to revise their own expectations about statistically probable vs. improbable events. An experimenter sampled a ball from a box of red and white balls and briefly displayed either a surprised or an unsurprised expression at the outcome before revealing it to the infant. Following an unsurprised expression, the results were consistent with prior work; infants looked longer at a statistically improbable outcome than a probable outcome. Following a surprised expression, however, this standard pattern disappeared or was even reversed. These results suggest that even before infants can observe the unexpected events themselves, they can use others' surprise to expect the unexpected. Starting early in life, human learners can leverage social information that signals others' prediction error to update their own predictions.

Feelings on feedback: Children's emotional responses during mathematics problem solving

Theories of learning emphasize the importance of both the cognitive and affective state of the learner. The current study focused on children's affective reactions to corrective feedback during mathematics problem solving. Eighty-seven elementary school children (M age = 7.6 years, 41% female, 68% White) solved mathematical equivalence problems during an online video call and received trial-by-trial feedback on their answers. Trained researchers used children's facial expressions, tone of voice, and verbal statements to quantify their positive and negative affect on each trial. Overall, children tended to express more positive affect than negative affect. However, negative affect was more prominent when the child was incorrect and received negative feedback, and higher negative affect was associated with lower accuracy and lower persistence on the task. These results provide novel empirical evidence for the role of emotions during children's STEM learning in a non-evaluative context.

A developmental perspective on feedback: How corrective feedback influences children's literacy, mathematics, and problem solving

Research in psychology and education indicates that corrective feedback can be a powerful learning tool. We provide a developmental perspective to focus specifically on how corrective feedback influences learning in childhood (~ages 3-11). Based on a systematic search, we review 44 empirical papers published between 1990 and 2022 examining the effects of corrective feedback on children's performance in the domains of literacy (n=18), mathematics (n=14), and problem solving (n=12). Across these domains, we synthesize research on how children respond to lessons and practice with, versus without, corrective feedback to provide theoretical and practical insights into (1) the effectiveness of corrective feedback in early childhood, (2) the features of effective feedback messages at different ages, and (3) the role of individual learner differences. We make several novel recommendations with some focused on future research questions and others focused on ways teachers can provide effective feedback to children.

Predicting pragmatic cue integration in adults' and children's inferences about novel word meanings

Language is learned in complex social settings where listeners must reconstruct speakers' intended meanings from context. To navigate this challenge, children can use pragmatic reasoning to learn the meaning of unfamiliar words. A critical challenge for pragmatic reasoning is that it requires integrating multiple information sources, which have typically been studied separately. Here we study this integration process. First, we experimentally isolate two sources of pragmatic information: expectations about informative communication and common ground. Next, we use a probabilistic model of conversational reasoning to formalize how these information sources should be combined and how this process might develop. We use this model to generate quantitative predictions, which we test against new experimental data from 3- to 5-year-old children (N = 243) and adults (N = 694). Results show close alignment between model predictions and data. Furthermore, the model provided a better explanation of the data compared with simpler alternative models assuming that participants selectively ignore one information source. This work integrates distinct sets of findings regarding information sources for early language learning and suggests that pragmatic reasoning models can provide a quantitative framework for understanding developmental changes in language learning. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Moderated Online Data-Collection for Developmental Research: Methods and Replications

Online data collection methods are expanding the ease and access of developmental research for researchers and participants alike. While its popularity among developmental scientists has soared during the COVID-19 pandemic, its potential goes beyond just a means for safe, socially distanced data collection. In particular, advances in video conferencing software has enabled researchers to engage in face-to-face interactions with participants from nearly any location at any time. Due to the novelty of these methods, however, many researchers still remain uncertain about the differences in available approaches as well as the validity of online methods more broadly. In this article, we aim to address both issues with a focus on moderated (synchronous) data collected using video-conferencing software (e.g., Zoom). First, we review existing approaches for designing and executing moderated online studies with young children. We also present concrete examples of studies that implemented choice and verbal measures (Studies 1 and 2) and looking time (Studies 3 and 4) across both in-person and online moderated data collection methods. Direct comparison of the two methods within each study as well as a meta-analysis of all studies suggest that the results from the two methods are comparable, providing empirical support for the validity of moderated online data collection. Finally, we discuss current limitations of online data collection and possible solutions, as well as its potential to increase the accessibility, diversity, and replicability of developmental science.

How young children integrate information sources to infer the meaning of words

Before formal education begins, children typically acquire a vocabulary of thousands of words. This learning process requires the use of many different information sources in their social environment, including their current state of knowledge and the context in which they hear words used. How is this information integrated? We specify a developmental model according to which children consider information sources in an age-specific way and integrate them via Bayesian inference. This model accurately predicted 2-5-year-old children's word learning across a range of experimental conditions in which they had to integrate three information sources. Model comparison suggests that the central locus of development is an increased sensitivity to individual information sources, rather than changes in integration ability. This work presents a developmental theory of information integration during language learning and illustrates how formal models can be used to make a quantitative test of the predictive and explanatory power of competing theories.

Erectile Dysfunction Is Highly Prevalent in Men With Newly Diagnosed Inflammatory Bowel Disease

BACKGROUND AND AIMS

Cross-sectional studies on sexual function in men with inflammatory bowel disease (IBD) yield mixed results. Using a prospective incidence cohort, we aimed to describe sexual function at baseline and over time and to identify factors associated with impaired sexual function in men with IBD.

METHODS

Men 18 years and older enrolled between April 2008 and January 2013 in the Ocean State Crohn's and Colitis Area Registry (OSCCAR) with a minimum of 2 years of follow-up were eligible for study. Male sexual function was assessed using the International Index of Erectile Function (IIEF), a self-administered questionnaire that assesses 5 dimensions of sexual function over the most recent 4 weeks. To assess changes in the IIEF per various demographic and clinical factors, linear mixed effects models were used.

RESULTS

Sixty-nine of 82 eligible men (84%) completed the questionnaire (41 Crohn's disease, 28 ulcerative colitis). The mean age (SD) of the cohort at diagnosis was 43.4 (19.2) years. At baseline, 39% of men had global sexual dysfunction, and 94% had erectile dysfunction. Independent factors associated with erectile dysfunction are older age and lower physical and mental component summary scores on the Short Form Health Survey (SF-36).

CONCLUSION

In an incident cohort of IBD patients, most men had erectile dysfunction. Physicians should be aware of the high prevalence of erectile dysfunction and its associated risk factors among men with newly diagnosed IBD to direct multidisciplinary treatment planning.

Opportunistic screening for bone disease using abdominal CT scans obtained for other reasons in newly diagnosed IBD patients

Bone disease is prevalent among patients with inflammatory bowel disease (IBD), though bone density screening remains underutilized. We used CT scans performed for other indications in IBD patients to identify and monitor osteopenia using CT attenuation values at the lumbar spine. Significant rates of bone disease were detected which would have otherwise gone undiagnosed.

INTRODUCTION

Osteoporosis affects about 14-42% of patients with IBD. Though screening is recommended in IBD patients with risk factors, it remains underutilized. In patients with newly diagnosed IBD, we used CT scans performed for other indications to identify and monitor progression of osteopenia.

METHODS

Using the Ocean State Crohn's and Colitis Area Registry, we identified adult patients with one or more abdominal CT scans. Each patient had two age- and gender-matched controls. Radiologists measured attenuation through trabecular bone in the L1 vertebral body recorded in Hounsfield units (HU). Generalized estimating equations were used to measure how HU varied as a function of gender, type of IBD, and age.

RESULTS

One hundred five IBD patients were included, and 72.4% were classified as "normal" bone mineral density (BMD) and 27.6% as potentially osteopenic: 8.6% with ulcerative colitis and 19.0% with Crohn's disease. We found a decrease in bone density over time (p < 0.001) and that BMD decreases more in Crohn's disease than in ulcerative colitis (p < 0.004). Sixty patients had two CT scans, and mean loss of 9.3 HU was noted. There was a non-significant decrease in BMD over time in patients exposed to > 31 days of steroids and BMD was stable with < 30 days of steroid exposure (p < 0.09).

CONCLUSION

Using CT scans obtained for other indications, we found low rates of osteopenia and osteoporosis that may otherwise have gone undiagnosed. Refinement of opportunistic screening may have advantages in terms of cost-savings and earlier detection of bone loss.

Vitamin D Status Is Associated with Intestinal Inflammation as Measured by Fecal Calprotectin in Crohn's Disease in Clinical Remission

BACKGROUND

Vitamin D, as potential immune modulator, has been implicated as an environmental risk factor for Crohn's disease (CD). Vitamin D status may be associated with disease risk, severity, activity, and progression. While associations between circulating 25OHD and markers of disease activity and inflammation in CD have been reported, the results are inconsistent.

AIM

To determine the association between vitamin D status and markers of disease activity and inflammation in CD.

METHODS

One hundred and nineteen CD patients' active and inactive diseases were enrolled in the cross-sectional study. Subject demographics and clinical data were collected. A serum sample was collected for 25OHD and CRP analysis, and a stool sample was collected for fecal calprotectin (FC) measurement.

RESULTS

The mean serum 25OHD concentration of the group was 59.8 (24.9) nmol/L. After controlling for confounding variables, serum 25OHD inversely correlated with FC (r = -0.207, P = 0.030), particularly among those in clinical remission (r = -0.242, P = 0.022). The association between FC and 25OHD was further confirmed by linear regression (r = 31.3 %, P < 0.001). FC was lower in patients with 25OHD levels ≥75 nmol/L compared with levels <25 nmol/L [FC: 32.2 (16.3-98.2) vs 100.0 (34.4-213.5) μg/g, P = 0.004]. In the current study, however, 25OHD was not significantly associated with either CRP or CDAI.

CONCLUSION

Circulating 25OHD was significantly inversely associated with intestinal inflammation as determined by FC in CD. Subgroup analysis confirmed the association among those in clinical remission, but not in those with active disease. 25OHD was not associated with disease activity score (CDAI) or systemic inflammation (CRP). Vitamin D intervention studies are warranted to determine whether raising serum 25OHD levels in patients with CD may reduce intestinal inflammation as measured by FC.

Fatigue is highly associated with poor health-related quality of life, disability and depression in newly-diagnosed patients with inflammatory bowel disease, independent of disease activity

BACKGROUND

Fatigue is common in Crohn's disease (CD) and ulcerative colitis (UC). Data on fatigue in newly diagnosed patients are unavailable.

AIM

To report prevalence of fatigue in newly diagnosed CD and UC patients and examine its association with health-related quality of life (HRQOL), depression and disability.

METHODS

The Ocean State Crohn's and Colitis Area Registry (OSCCAR) is a statewide cohort of newly diagnosed inflammatory bowel disease patients in Rhode Island. Fatigue was assessed using the Functional Assessment of Chronic Illness Therapy-Fatigue Scale. Patients were administered instruments measuring HRQOL, overall disability and work impairment, and depression.

RESULTS

Fatigue was prevalent in 26.4% of 220 subjects. Cohen's d effect sizes for fatigue were large: Short-Form 36 Health Survey mental health component (CD 1.5, UC 1.4) and physical health component (CD 1.4, UC 1.4), EuroQol-5D valuation of current health state (CD 1.2, UC 1.0), Inflammatory Bowel Disease Questionnaire (CD 1.9, UC 1.6) and Patient Health Questionnaire depression scale (CD 1.8, UC 1.7). Fatigued patients reported more work impairment (Score difference: CD 29.5%, UC 23.8%) and activity impairment (score difference: CD 32.3%, UC 25.7%) on the Work Productivity and Activity Impairment Questionnaire. Fatigue's association with all scores remained highly significant despite controlling for disease activity.

CONCLUSIONS

Fatigue is strongly associated with poor HRQOL, disability and depression similarly in CD and UC even when controlling for disease activity. Fatigue's association with a wide range of patient-reported outcome measures suggests that monitoring fatigue is a simple way to screen for overall disruption in patient life.

The Escherichia coli AmtB protein as a model system for understanding ammonium transport by Amt and Rh proteins

The Escherichia coli ammonium transport protein (AmtB) has become the model system of choice for analysis of the process of ammonium uptake by the ubiquitous Amt family of inner membrane proteins. Over the past 6 years we have developed a range of genetic and biochemical tools in this system. These have allowed structure/function analysis to develop rapidly, offering insight initially into the membrane topology of the protein and most recently leading to the solution of high-resolution 3D structures. Genetic analysis has revealed a novel regulatory mechanism that is apparently conserved in prokaryotic Amt proteins and genetic approaches are also now being used to dissect structure/function relationships in Amt proteins. The now well-recognised homology between the Amt proteins, found in archaea, eubacteria, fungi and plants, and the Rhesus proteins, found characteristically in animals, also means that studies on E. coli AmtB can potentially shed light on structure/function relationships in the clinically important Rh proteins.

Complex formation between AmtB and GlnK: an ancestral role in prokaryotic nitrogen control

Ammonium transport proteins belonging to the Amt family are ubiquitous in prokaryotes. In Escherichia coli, the AmtB protein and the associated P(II) signal transduction protein (GlnK) have recently been recognized as an ammonium sensory system that effectively couples the intracellular nitrogen regulation (Ntr) system to external changes in ammonium availability. Given the almost invariant coupling of AmtB and GlnK in bacteria and archaea it seems probable that these two proteins may constitute an ancestral nitrogen-responsive system that has been coupled with a variety of unrelated nitrogen regulatory processes, which are now found in prokaryotes. The multiplicity of P(II) proteins could therefore be considered to have evolved from an ancestral GlnK-like protein and to have subsequently been adapted to control many other aspects of nitrogen metabolism.

P(II) signal transduction proteins, pivotal players in microbial nitrogen control

The P(II) family of signal transduction proteins are among the most widely distributed signal proteins in the bacterial world. First identified in 1969 as a component of the glutamine synthetase regulatory apparatus, P(II) proteins have since been recognized as playing a pivotal role in control of prokaryotic nitrogen metabolism. More recently, members of the family have been found in higher plants, where they also potentially play a role in nitrogen control. The P(II) proteins can function in the regulation of both gene transcription, by modulating the activity of regulatory proteins, and the catalytic activity of enzymes involved in nitrogen metabolism. There is also emerging evidence that they may regulate the activity of proteins required for transport of nitrogen compounds into the cell. In this review we discuss the history of the P(II) proteins, their structures and biochemistry, and their distribution and functions in prokaryotes. We survey data emerging from bacterial genome sequences and consider other likely or potential targets for control by P(II) proteins.

The Rhizobium leguminosarum glnB gene is down-regulated during symbiosis

Symbiotic nitrogen fixation involves the development, on the legume plant root, of specialised organs called nodules, within which plant photosynthates are exchanged for combined nitrogen of bacterial origin. The glnB gene encodes a signal transduction protein (P(II)) which is a component of the bacterial nitrogen regulation (Ntr) system and an essential regulator of ammonium assimilation. We demonstrate that in Rhizobium leguminosarum the glnB promoter is strongly regulated by nitrogen and NtrC, but still shows a significant level of activity in conditions of nitrogen excess. Expression of genes involved in nitrogen assimilation has been shown to be absent in nitrogen-fixing bacteroids, and, in agreement with this, we find that the glnB promoter is down-regulated during bacteroid differentiation at a time coincident with the arrest of bacterial division in the nodule. This pattern is common to other bacterial genes involved in nitrogen assimilation and it is noteworthy that the zone where the glnB promoter is active is coincident with the region in which NtrC is expressed.

Two residues in the T-loop of GlnK determine NifL-dependent nitrogen control of nif gene expression

X-ray crystallographic analysis of the Escherichia coli P(II) protein paralogues GlnB and GlnK has shown that they share a superimposable structural core but can differ in conformation of the T-loop, a region of the protein (residues 37-54) that has been shown to be important for interaction with other proteins. In Klebsiella pneumoniae GlnK has been shown to have a clearly defined function in regulating NifL-mediated inhibition of NifA activity in response to the nitrogen status, and GlnB, when expressed from the chromosome, does not substitute for GlnK. Because the T-loops of K. pneumoniae and E. coli GlnB and GlnK differ at just three residues, 43, 52, and 54, we have used a previously constructed heterologous system, in which K. pneumoniae nifLA is expressed in E. coli, to investigate the importance of GlnK residues 43, 52, and 54 for regulation of the NifLA interaction. By site-directed mutagenesis of glnB we have shown that residue 54 is the single most important amino acid in the T-loop in the context of the regulation of NifA activity. Furthermore, a combination of just two changes, in residues 54 and 43, allows GlnB to function as GlnK and completely relieve NifL inhibition of NifA activity.

Inhibition of glutamine synthetase II expression by the product of the gstI gene

We report the identification of a previously unrecognized gene that is involved in the regulation of the Rhizobium leguminosarum glnII (glutamine synthetase II) gene. This gene, which is situated immediately upstream of glnII, was identified by means of a deletion/complementation analysis performed in the heterologous background of Klebsiella pneumoniae. It has been designated gstI (glutamine synthetase translational Inhibitor) because, when a complete version of gstI is present, it is possible to detect glnII-specific mRNA, but neither GSII activity nor GSII protein. The gstI gene encodes a small (63 amino acids) protein, which acts in cis or in trans with respect to glnII and is transcribed divergently with respect to glnII from a promoter that was found to be strongly repressed by the nitrogen transcriptional regulator NtrC. A mutated version of GstI lacking the last 14 amino acids completely lost its capacity to repress glnII expression. Our results indicate that gstI mediates the translation inhibition of glnII mRNA and, based on in silico analyses, a mechanism for GstI action is proposed.

Membrane topology of the Mep/Amt family of ammonium transporters

The Mep/Amt proteins constitute a new family of transport proteins that are ubiquitous in nature. Members from bacteria, yeast and plants have been identified experimentally as high-affinity ammonium transporters. We have determined the topology of AmtB, a Mep/Amt protein from Escherichia coli, as a representative protein for the complete family. This was established using a minimal set of AmtB-PhoA fusion proteins with a complementary set of AmtB-LacZ fusions. These data, accompanied by an in silico analysis, indicate that the majority of the Mep/Amt proteins contain 11 membrane-spanning helices, with the N-terminus on the exterior face of the membrane and the C-terminus on the interior. A small subset, including E. coli AmtB, probably have an additional twelfth membrane-spanning region at the N-terminus. Addition of PhoA or LacZ alpha-peptide to the C-terminus of E. coli AmtB resulted in complete loss of transport activity, as judged by measurements of [14C]-methylammonium uptake. This C-terminal region, along with four membrane-spanning helices, contains multiple residues that are conserved within the Mep/Amt protein family. Structural modelling of the E. coli AmtB protein suggests a number of secondary structural features that might contribute to function, including a putative ammonium binding site on the periplasmic face of the membrane at residue Asp-182. The implications of these results are discussed in relation to the structure and function of the related human Rhesus proteins.

The role of region II in the RNA polymerase sigma factor sigma(N) (sigma(54))

Bacterial RNA polymerase holoenzymes containing the sigma subunit sigma(N) (sigma(54)) can form a stable closed complex with promoter DNA but only undergo transition to an open complex and transcription initiation when acted on by an activator protein. Proteins of the sigma(N) family have a conserved N-terminal region of 50 amino acids (Region I) that is separated from a conserved C-terminal region of around 360 amino acids (Region III) by a much more variable sequence of between 30 and 110 residues (Region II). We have investigated the role of Region II in Klebsiella pneumoniae sigma(N) by studying the properties of deletions of all or part of the region both in vivo and in vitro. We found that whilst Region II is not essential, deletion of all or part of it can significantly impair sigma(N) activity. Deletions have effects on DNA binding by the isolated sigma factor and on holoenzyme formation, but the most marked effects are on transition of the holoenzyme from the closed to the open complex in the presence of the activator protein.

Studies on the roles of GlnK and GlnB in regulating Klebsiella pneumoniae NifL-dependent nitrogen control

In Klebsiella pneumoniae, nitrogen fixation (nif) genes are regulated in response to fixed nitrogen and oxygen. The activity of the nif-specific transcriptional activator NifA is modulated by NifL, which mediates both oxygen and nitrogen control. The signal transduction protein GlnK is required to relieve the inhibitory effect of NifL on NifA that occurs when the intracellular N status is high and in a wild-type cell, the action of GlnK cannot be substituted by the structurally related protein PII. We have studied the modulation of NifA activity by NifL in an heterologous system in which the host organism is Escherichia coli. Using a DeltaglnB, DeltaglnK mutant, we have shown that the modulation of NifA activity by NifL is dependent on the concentration of GlnK in the cell and that when overproduced, PII can substitute for GlnK. Furthermore, our data suggest that PII can counteract the positive action of GlnK in relieving NifL-dependent inhibition of NifA activity. This negative effect of PII may be physiologically important in establishing repression of nif gene expression when the intracellular nitrogen status rises.

The signal transduction protein GlnK is required for NifL-dependent nitrogen control of nif gene expression in Klebsiella pneumoniae

In Klebsiella pneumoniae, transcription of the nitrogen fixation (nif) genes is regulated in response to molecular oxygen or availability of fixed nitrogen by the coordinated activities of the nifA and nifL gene products. NifA is a nif-specific transcriptional activator, the activity of which is inhibited by interaction with NifL. Nitrogen control of NifL occurs at two levels: transcription of the nifLA operon is regulated by the global ntr system, and the inhibitory activity of NifL is controlled in response to fixed nitrogen by an unknown factor. K. pneumoniae synthesizes two PII-like signal transduction proteins, GlnB, which we have previously shown not to be involved in the response of NifL to fixed nitrogen, and the recently identified protein GlnK. We have now cloned the K. pneumoniae glnK gene, studied its expression, and shown that a null mutation in glnK prevents NifL from responding to the absence of fixed nitrogen, i.e., from relieving the inhibition of NifA activity. Hence, GlnK appears to be involved, directly or indirectly, in NifL-dependent regulation of nif gene expression in K. pneumoniae. Comparison of the GlnB and GlnK amino acid sequences from six species of proteobacteria identifies five residues (residues 3, 5, 52, 54, and 64) which serve to distinguish the GlnB and GlnK proteins.

The Rhizobium etli amtB gene coding for an NH4+ transporter is down-regulated early during bacteroid differentiation

During development of root nodules, Rhizobium bacteria differentiate inside the invaded plant cells into N2-fixing bacteroids. Terminally differentiated bacteroids are unable to grow using the ammonia (NH3) produced therein by the nitrogenase complex. Therefore, the nitrogen assimilation activities of bacteroids, including the ammonium (NH4+) uptake activity, are expected to be repressed during symbiosis. By sequence homology the R. etli amtB (ammonium transport) gene was cloned and sequenced. As previously shown for its counterpart in other organisms, the R. etli amtB gene product mediates the transport of NH4+. The amtB gene is cotranscribed with the glnK gene (coding for a PII-like protein) from a nitrogen-regulated sigma 54-dependent promoter, which requires the transcriptional activator NtrC. Expression of the glnKamtB operon was found to be activated under nitrogen-limiting, free-living conditions, but down-regulated just when bacteria are released from the infection threads and before transcription of the nitrogenase genes. Our data suggest that the uncoupling between N2-fixation and NH3 assimilation observed in symbiosomes is generated by a transcriptional regulatory mechanism(s) beginning with the inactivation of NtrC in younger bacteroids.

The RpoN-box motif of the RNA polymerase sigma factor sigma N plays a role in promoter recognition

The RNA polymerase sigma factor sigma N (sigma 54) is characterized by the presence, near the C-terminal end of the protein, of a highly conserved sequence of 10 amino acids (ARRTVAKYRE) that has been termed the RpoN box. In order to examine the function of this motif, which is predicted to adopt an alpha-helical structure, we have isolated a number of mutations that alter residues within the box and examined the properties of the sigma N derivatives encoded by them. Certain mutations that alter charged and potentially exposed residues within the motif result in transcriptionally inactive proteins with impaired promoter recognition but no impairment in core RNA polymerase binding. We therefore suggest that the RpoN box could play a direct or indirect role in recognition of the -24, -12 promoter consensus that is characteristic of sigma N-dependent genes.

The role of uridylyltransferase in the control of Klebsiella pneumoniae nif gene regulation

The glnD gene in enteric bacteria encodes a uridylyltransferase/uridylyl-removing enzyme which acts as the primary nitrogen sensor in the nitrogen regulation (Ntr) system. We have investigated the role of this enzyme in transcriptional regulation of nitrogen fixation genes in Klebsiella pneumoniae by cloning glnD from this organism and constructing a null mutant by insertional inactivation of the chromosomal gene using the omega interposon. K. pneumoniae glnD encodes a 102.3 kDa polypeptide which is highly homologous to the predicted products of both Escherichia coli glnD and Azotobacter vinelandii nfrX. The glnD-omega mutant was unable to uridylylate PII and was altered in adenylylation/deadenylylation of glutamine synthetase. Uridylyltransferase was required for derepression of ntr-regulated promoters such as glnAp2 and pnifL but was not involved in the nif-specific response to changes in nitrogen status mediated by the nifL product. We conclude that a separate, as yet uncharacterised, nitrogen control system may be responsible for nitrogen sensing by NifL.

Nurse manager performance appraisal: a collaborative approach

The job description and performance appraisal criteria for the Clinical Nurse Manager (CNM) were revised to provide clarity of role responsibilities and promote collegiality. The new formats reflected much better the complexities and differences existing in the 15 distinct inpatient and ambulatory practice settings. Six categories were defined which summarized the CNM role and a qualitative tool was developed for performance evaluation.

Characterisation of mutations in the Klebsiella pneumoniae nitrogen fixation regulatory gene nifL which impair oxygen regulation

The nifL gene product of Klebsiella pneumoniae inhibits the activity of the positive activator protein NifA in response to increased levels either of fixed nitrogen or of oxygen in the medium. In order to demonstrate that the responses to these two effectors are discrete we have subjected nifL to hydroxylamine mutagenesis and isolated nifL mutants that are impaired in their ability to respond to oxygen but not to fixed nitrogen. Two such mutations were sequenced and shown to be single base pair changes located in different parts of nifL. The amino acid sequence of NifL shows limited homology to the histidine protein kinases which comprise the sensing component of bacterial two-component regulatory systems. In the light of the location of one of the oxygen-insensitive mutations (Leu294Phe) we have reassessed this homology and we suggest that the Gln273-Leu317 region of NifL may facilitate interactions between NifL and NifA.

The helix-turn-helix motif of sigma 54 is involved in recognition of the -13 promoter region

Residue Arg-383 in the proposed helix-turn-helix motif of the novel RNA polymerase sigma factor sigma 54 has been changed by site-directed mutagenesis to all possible alternative amino acids. Only two mutants, RK383 and RH383, are active in promoting transcription from either the glnAp2 promoter or the nifL promoter. We constructed a set of mutant derivatives of glnAp2 such that each base in the conserved GG and GC doublets at -24 and -12 was changed to all possible alternatives. All 12 mutant glnAp2 promoters showed a marked promoter-down phenotype with wild-type sigma 54, but RK383 suppressed changes of both G to C and G to T at -13. This result suggests that the sigma 54 helix-turn-helix is involved in recognition of the -13 region of sigma 54-dependent promoters.

Localization of the glnD gene on a revised map of the 200-kilobase region of the Escherichia coli chromosome

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The product of the nitrogen fixation regulatory gene nfrX of Azotobacter vinelandii is functionally and structurally homologous to the uridylyltransferase encoded by glnD in enteric bacteria

We sequenced the nitrogen fixation regulatory gene nfrX from Azotobacter vinelandii, mutations in which cause a Nif- phenotype, and found that it encodes a 105-kDa protein (NfrX), the N terminus of which is highly homologous to that of the uridylyltransferase-uridylyl-removing enzyme encoded by glnD in Escherichia coli. In vivo complementation experiments demonstrate that the glnD and nfrX products are functionally interchangeable. A vinelandii nfrX thus appears to encode a uridylyltransferase-uridylyl-removing enzyme, and in this paper we report the first sequence of such a protein. The Nif- phenotype of nfrX mutants can be suppressed by a second mutation in a recently identified nifL-like gene immediately upstream of nifA in A. vinelandii. NifL mediates nif regulation in response to the N status in A. vinelandii, presumably by inhibiting NifA activator function as occurs in Klebsiella pneumoniae; thus, one role of NfrX is to modify, either directly or indirectly, the activity of the nifL product.

The roles of the nifW, nifZ and nifM genes of Klebsiella pneumoniae in nitrogenase biosynthesis

Active Fe protein of nitrogenase was synthesised in a non-nitrogen fixing organism when Escherichia coli was transformed with a plasmid encoding only two nif-specific genes, nifH and nifM of Klebsiella pneumoniae. Hence proteins NifH and NifM are sufficient to produce active Fe protein in E. coli. K. pneumoniae strains carrying chromosomal nifW- and nifZ- mutations were constructed and shown to be significant C2H2-reducing activity and to grow on N-free plates. Nevertheless, derepressing cultures of the mutant strains had reduced levels of MoFe protein activity, and consequently significantly lower levels of nitrogenase activity, than the nif+ parent strain. NifW and NifZ therefore appear to be involved in the formation or accumulation of active MoFe protein, but are not essential for nitrogen fixation in K. pneumoniae under the conditions tested.

Identification of the Klebsiella pneumoniae glnB gene: nucleotide sequence of wild-type and mutant alleles

The glnB gene of Klebsiella pneumoniae, which encodes the nitrogen regulation protein PII, has been cloned and sequenced. The gene encodes a 12429 dalton polypeptide and is highly homologous to the Escherichia coli glnB gene. The sequences of a glnB mutation which causes glutamine auxotrophy and of a Tn5 induced Gln+ suppressor of this mutation were also determined. The glutamine auxotrophy was deduced to be the result of a modification of the uridylylation site of PII, and the suppression was shown to be caused by Tn5 insertion in glnB. The 3' end of an open reading frame of unknown function was identified upstream of glnB and may be part of an operon containing glnB. Potential homologues of glnB encoding polypeptides extremely similar in sequence to PII were identified upstream of published sequences of the glutamine synthetase structural gene (glnA) in Rhizobium leguminosarum, Bradyrhizobium japonicum and Azospirillum brasilense.

The nucleotide sequence of the nifM gene of Klebsiella pneumoniae and identification of a new nif gene: nifZ

A 1.4-kb PstI-HpaI DNA fragment carrying the Klebsiella pneumoniae nifM gene has been sequenced; nifM has been shown to encode a 30.6-kDa polypeptide. Two other open-reading frames were identified upstream of nifM. The one immediately upstream of nifM encodes a 16.6-kDa polypeptide which has been identified by in vitro transcription/translation in an Escherichia coli 30,000 x g supernatant system; we propose to designate this gene nifZ. The sequence of the second open reading frame is incomplete but it does not correspond to nifV, the gene previously thought to be immediately upstream of nifM, and may therefore identify another new nif gene. Both nifM and nifZ have functional nif promoters with the characteristic-24, -12 consensus sequence, we find no evidence for a nifM upstream activator sequence. The role of nifZ in nitrogenase biosynthesis is unknown but its identification calls into question previous assertions that only nifM and nifH are required for the synthesis of nitrogenase Fe protein.

The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: analysis of conserved sequences in NtrA proteins

The nucleotide sequence of the Azotobacter vinelandii ntrA gene has been determined. It encodes a 56916 Dalton acidic polypeptide (AvNtrA) with substantial homology to NtrA from Klebsiella pneumoniae (KpNtrA) and Rhizobium meliloti (RmNtrA). NtrA has been shown to act as a novel RNA polymerase sigma factor but the predicted sequence of AvNtrA substantiates our previous analysis of KpNtrA in showing no substantial homology to other known sigma factors. Alignment of the predicted amino acid sequences of AvNtrA, KpNtrA and RmNtrA identified three regions; two showing greater than 50% homology and an intervening sequence of less than 10% homology. The predicted protein contains a short sequence near the centre with homology to a conserved region in other sigma factors. The C-terminal region contains a region of homology to the beta' subunit of RNA polymerase (RpoC) and two highly conserved regions one of which is significantly homologous to known DNA-binding motifs. In A. vinelandii, ntrA is followed by another open reading frame (ORF) which is highly homologous to a comparable ORF downstream of ntrA in K. pneumoniae and R. meliloti.

Interaction of purified NtrC protein with nitrogen regulated promoters from Klebsiella pneumoniae

The product of the Klebsiella pneumoniae nitrogen regulatory gene ntrC has been purified and shown to be a dimeric protein of subunit molecular weight 54Kd, designated NtrC. In an in vitro coupled transcription-translation system NtrC inhibited expression from both the ntrBC and glnA promoters. NtrC bound to both of these ntr repressible promoters with equal affinity, but did not bind to the activatable nitrogen fixation promoters nifF or nifLA. NtrC makes contact with nucleotides flanking the -10 region of the glnA (RNA2) promoter at sequences homologous with the proposed consensus binding site.

The nucleotide sequence of the nitrogen regulation gene ntrB and the glnA-ntrBC intergenic region of Klebsiella pneumoniae

The nucleotide sequence of the Klebsiella pneumoniae ntrB gene and the glnA-ntrBC intergenic region has been determined. NtrB encodes a 38,409 Dalton polypeptide with a potential DNA-binding domain between residues 67 and 86. This N-terminal domain may play a role in the co-operative control of ntr-regulated promoters by the ntrB and ntrC products. Mapping of in vivo transcripts with S1 nuclease identified three transcripts in the glnA-ntrBC intergenic region. Two transcripts originate upstream of glnA; one reading through into ntrBC and one terminating at a sequence resembling a rho-independent terminator between glnA and ntrBC. A third transcript originates from the ntrBC promoter which has a consensus binding site for the ntrC product in the -10 region. Comparison of the glnA-ntrBC intergenic sequences from K. pneumoniae, Escherichia coli and Salmonella typhimurium has identified a number of conserved features and some significant differences.

Positive and negative control of the glnA ntrBC regulon in Klebsiella pneumoniae

The nitrogen regulation system of Klebsiella pneumoniae comprises three genes ntrA, ntrB and ntrC. We have found that the glnA ntrBC regulon in K. pneumoniae has a similar structure, P1 glnA P2 ntrBC, to that in other enterobacteria. We have constructed plasmids with glnA and ntrB translational lacZ fusions and measured expression from P1 and/or P2 in a K. pneumoniae delta (glnA ntrBC) background with different plasmids which provided the ntrB, ntrC or nifA products in trans. These studies demonstrate that, as in other enterobacteria, transcription of ntrBC is from P1 under nitrogen deficiency and from P2 under nitrogen excess. The P1 promoter can be regulated both positively and negatively; activation requires both ntrB and ntrC products but the ntrC product is sufficient to repress. The P2 promoter is negatively controlled by the ntrC product. Comparison of the modes of regulation of P1 and P2 with regulation of the promoter of the nifLA operon leads us to suggest that these may represent three different classes of ntr-regulated promoters. Although previous studies have shown that the nifA product can substitute for the ntrC product as a positive activator of transcription for a number of promoters, we find that nifA product cannot substitute for ntrC product as a negative regulator at P1 or P2.

Positive control and autogenous regulation of the nifLA promoter in Klebsiella pneumoniae

The nitrogen fixation (nif) genes of Klebsiella pneumoniae are specifically regulated by the products of the nifLA operon. We have located the promoter of this operon, and identified sequences required for nifLA transcription. Transcription from this promoter is shown to be positively regulated by the ntrC gene product (which coordinates the expression of many operons required for nitrogen assimilation) and also autogenously by the product of the nifA gene.

Cloning and characterisation of nifLA regulatory mutations from Klebsiella pneumoniae

A total of nine regulatory mutations in the nifLA operon of Klebsiella pneumoniae were cloned in the high copy-number plasmid vector pACYC184. The regulatory phenotypes of the resultant clones were then correlated with their restriction maps and their ability to synthesise nifL and nifA polypeptides in vivo. One mutation, nifL2401, was identified as a 400 bp. deletion within the nifL gene. This mutation was non-polar and caused a Nif+ phenotype which showed escape from repression by oxygen and low levels of fixed nitrogen. Identification of this deletion allows the first definitive allocation of a mutation with this phenotype to the nifL gene and provides further evidence for the role of the nifL gene product in nif-specific repression.

Cloning of the glnA, ntrB and ntrC genes of Klebsiella pneumoniae and studies of their role in regulation of the nitrogen fixation (nif) gene cluster

The glnA, ntrB and ntrC genes of Klebsiella pneumoniae have been cloned, on a 12 kb HindIII fragment, into the plasmid pACYC184. In a coupled in vitro transcription/translation system the resultant plasmid, pGE100, directed synthesis of five polypeptides (molecular weights 73, 53, 51, 39, 36 kd) from the cloned fragment. A number of plasmids were derived from pGE100 and studied by complementation analysis and in vitro transcription/translation in order to locate particular genes and identify their products. On the basis of the results presented here, together with previous genetic and physical characterisation of the glnA gene and its product in other enteric bacteria, we propose that the 53 kd polypeptide is the glnA gene product (glutamine synthetase monomer). Two polypeptides (36 kd and 51 kd) were synthesised from a 3 kb region previously defined as glnR. In E. coli and S. typhimurium this region comprises two genes ntrB and ntrC with products of 36 kd and 54 kd respectively. This analogy supports the idea that the 36 kd and 51 kd polypeptides are the products of the K. pneumoniae ntrB and ntrC genes respectively. Comparison of these assignments with the physical map of the region indicates a gene order glnA, ntrB, ntrC. Assessment of the Nif phenotype of a glnA-ntrC deletion strain carrying various clones from pGE100 demonstrated that glnA is not required for expression of the nif regulon and that of the three genes cloned, ntrC alone is sufficient for nif expression.

Complementation analysis of glnA-linked mutations which affect nitrogen fixation in Klebsiella pneumoniae

A number of mutants have been isolated which affect regulation of the nitrogen fixation (nif) gene cluster in Klebsiella pneumoniae and all of which are linked to glnA, the structural gene for glutamine synthetase (G.S.). These mutants were classified on the basis of their G.S. and nitrogenase activities in conditions of nitrogen limitation and excess. The plasmid R68.45 was then used to generate a number of R-primes carrying the glnA region of the K. pneumoniae chromosome. One of these R-primes (pGE10) was subsequently used in complementation analysis and by isolation of transposon-induced insertion mutations in pGE10 we have demonstrated the existence of a gene, glnG, closely linked to glnA. Mutations in glnG have a similar phenotype to glnG mutants described in Escherichia coli (Pahel and Tyler 1979) and Salmonella typhimurium (Kustu et al. 1979) in that substantially reduce G.S. activity but are not glutamine auxotrophs. GlnG mutants have very low nitrogenase activity indicating that the glnG product may be involved regulation of the nif gene cluster in K. pneumoniae.

Analysis of regulation of Klebsiella pneumoniae nitrogen fixation (nif) gene cluster with gene fusions

Gene fusions in which the lac genes are under the control of each promoter in the Klebsiella pneumoniae, nitrogen fixation (nif) gene cluster have been constructed. These fusions have been used to examine positive control of the cluster and the response of individual genes to repression by ammonia and oxygen. De-repression of nif transcriptional units is coordinate and molybdate is required for maximal expression of the structural gene operon, which is autogenously regulated.

The use of translocatable genetic elements to construct a fine-structure map of the Klebsiella pneumoniae nitrogen fixation (nif) gene cluster

The transposons Tn5, Tn7 and Tn10 and bacteriophage Mu have been used to derive insertion mutations in the Klebsiella pneumoniae nif gene cluster. A large number of deletion mutants have been derived by imprecise excision of insertion mutations and these deletions have been used to construct a fine-structure map of the nif cluster. Comparison of this genetic map with a physical map of the nif cluster derived by Reidel et al. (1979) showed a very good correlation between genetic and physical mapping methods. A new complementation group, designated nifU, has been identified and mapped between nifN and nifS. Polarity studies on the 14 nif cistrons now identified suggests that they are organized in at least seven transcriptional units and that all the multicistronic units are transcribed in the same direction.

Polarity of mutations induced by insertion of transposons Tn5, Tn7 and Tn10 into the nif gene cluster of Klebsiella pneumoniae

Three new genes nifM, nifI and nifN have been mapped in the nif gene cluster of Klebsiella pneumoniae and a fourth gene nifJ has been confirmed as being a separate cistron. Polar nif mutations were obtained by transposition of Tn7 to plasmid pRD1, and of Tn5 and Tn10 to plasmid pMF100, a derivative of pRD1. Complementation analysis of the nif::Tn mutants led to the identification of at least six transcriptional units: nifB; nifA; nifJ; nifH, nifD and nifK; nifE and nifI; nifN, nifM and nifF. Biochemical and genetic evidence suggest that the three genes nifH, nifD and nifK, which are probably the structural genes for nitrogenase, belong to the same operon and are transcribed from nifH to nifK. A polypeptide with a molecular weight of approximately 120,000 is presumed to be the nifJ product.

Complementation analysis of Klebsiella pneumoniae mutants defective in nitrogen fixation

A series of mutants defective in nitrogen fixation (nif) were isolated in Klebsiella pneumoniae strain M5a1. The nif mutations were either located on plasmid pRD1 or on the K. pneumoniae chromosome. A total of 37 plasmid mutants and 28 chromosomal mutants were employed in complementation tests using the acetylene reduction technique. Most mutants could be assigned to one of seven nif cistrons: nifA, nifB, nifD, nifE, nifF, nifH, and nifK. Complementation analysis of two nif deletion mutants confirmed transductional evidence that these strains carry nifB-A-F deletions. One deletion mutant had, in contrast to previous transductional analysis, a functional nifK cistron and presumably is deleted for nifB-A-F-E. Examination of the biochemical phenotype of several mutants suggests that the nifA product has a regulatory function, and nifK, nifD and nifH are most probably the structural genes for nitrogenase.