Identifying the Gene Regulatory Network of the Starvation-Induced Transcriptional Activator Nla28.

Myxococcus xanthus copes with starvation by producing fruiting bodies filled with dormant and stress-resistant spores. Here, we aimed to better define the gene regulatory network associated with Nla28, a transcriptional activator/enhancer binding protein (EBP) and a key regulator of the early starvation response. Previous work showed that Nla28 directly regulates EBP genes that are important for fruiting body development. However, the Nla28 regulatory network is likely to be much larger because hundreds of starvation-induced genes are downregulated in a nla28 mutant strain. To identify candidates for direct Nla28-mediated transcription, we analyzed the downregulated genes using a bioinformatics approach. Nine potential Nla28 target promoters (29 genes) were discovered. The results of in vitro promoter binding assays, coupled with in vitro and in vivo mutational analyses, suggested that the nine promoters along with three previously identified EBP gene promoters were indeed in vivo targets of Nla28. These results also suggested that Nla28 used tandem, imperfect repeats of an 8-bp sequence for promoter binding. Interestingly, eight of the new Nla28 target promoters were predicted to be intragenic. Based on mutational analyses, the newly identified Nla28 target loci contained at least one gene that was important for starvation-induced development. Most of these loci contained genes predicted to be involved in metabolic or defense-related functions. Using the consensus Nla28 binding sequence, bioinformatics, and expression profiling, 58 additional promoters and 102 genes were tagged as potential Nla28 targets. Among these putative Nla28 targets, functions, such as regulatory, metabolic, and cell envelope biogenesis, were assigned to many genes. IMPORTANCE In bacteria, starvation leads to profound changes in behavior and physiology. Some of these changes have economic and health implications because the starvation response has been linked to the formation of biofilms, virulence, and antibiotic resistance. To better understand how starvation contributes to changes in bacterial physiology and resistance, we identified the putative starvation-induced gene regulatory network associated with Nla28, a transcriptional activator from the bacterium Myxoccocus xanthus. We determined the mechanism by which starvation-responsive genes were activated by Nla28 and showed that several of the genes were important for the formation of a highly resistant cell type.

Profiling Myxococcus xanthus Swarming Phenotypes through Mutation and Environmental Variation.

Myxococcus xanthus is a bacterium that lives on surfaces as a predatory biofilm called a swarm. As a growing swarm feeds on prey and expands, it displays dynamic multicellular patterns such as traveling waves called ripples and branching protrusions called flares. The rate at which a swarm expands across a surface, and the emergence of the coexisting patterns, are all controlled through coordinated cell movement. M. xanthus cells move using two motility systems known as adventurous (A) and social (S). Both are involved in swarm expansion and pattern formation. In this study, we describe a set of M. xanthus swarming genotype-to-phenotype associations that include both genetic and environmental perturbations. We identified new features of the swarming phenotype, recorded and measured swarm expansion using time-lapse microscopy, and compared the impact of mutations on different surfaces. These observations and analyses have increased our ability to discriminate between swarming phenotypes and provided context that allows us to identify some phenotypes as improbable outliers within the M. xanthus swarming phenome. IMPORTANCE Myxococcus xanthus grows on surfaces as a predatory biofilm called a swarm. In nature, a feeding swarm expands by moving over and consuming prey bacteria. In the laboratory, a swarm is created by spotting cell suspension onto nutrient agar in lieu of prey. The suspended cells quickly settle on the surface as the liquid is absorbed into the agar, and the new swarm then expands radially. An assay that measures the expansion rate of a swarm of mutant cells is the first, and sometimes only, measurement used to decide whether a particular mutation impacts swarm motility. We have broadened the scope of this assay by increasing the accuracy of measurements and introducing prey, resulting in new identifiable and quantifiable features that can be used to improve genotype-to-phenotype associations.

School readiness of children with language impairment: predicting literacy skills from pre-literacy and social-behavioural dimensions.

BACKGROUND: School readiness generally captures the notion that children do best when they arrive at formal schooling with a certain threshold of skill that will help them thrive in the classroom's academic and social milieu. AIMS: To examine the dimensionality of the construct of school readiness among children with language impairment (LI), as well as the extent to which these dimensions relate to children's end-of-kindergarten literacy skills. METHODS & PROCEDURES: Participants were 136 preschool-aged children with LI. Children were assessed on measures of pre-literacy, social, and behavioural skills in preschool and reading and spelling in kindergarten. OUTCOMES & RESULTS: Confirmatory factor analyses indicated that school readiness for this sample of children with LI is best characterized as two dimensions: pre-literacy and socio-emotional. Of the two dimensions, pre-literacy readiness was predictive of children's future performance in reading and spelling. CONCLUSIONS & IMPLICATIONS: The results further our theoretical understanding of the dimensions of school readiness, as well as our knowledge of how these skills are related among children with LI. Identifying domain-specific readiness skills that are predictive of kindergarten success can help to identify means of early assessment and targets for speech-language intervention.

The 'robustness' of vocabulary intervention in the public schools: targets and techniques employed in speech-language therapy.

This study examined vocabulary intervention-in terms of targets and techniques-for children with language impairment receiving speech-language therapy in public schools (i.e., non-fee-paying schools) in the United States. Vocabulary treatments and targets were examined with respect to their alignment with the empirically validated practice of rich vocabulary intervention. Participants were forty-eight 5-7-year-old children participating in kindergarten or the first-grade year of school, all of whom had vocabulary-specific goals on their individualized education programmes. Two therapy sessions per child were coded to determine what vocabulary words were being directly targeted and what techniques were used for each. Study findings showed that the majority of words directly targeted during therapy were lower-level basic vocabulary words (87%) and very few (1%) were academically relevant. On average, three techniques were used per word to promote deep understanding. Interpreting findings against empirical descriptions of rich vocabulary intervention indicates that children were exposed to some but not all aspects of this empirically supported practice.

Go Beyond Compliance: Use Individualized Education Programs to Answer Strategic Questions and Improve Programs.

PURPOSE: The most significant document to ensure effective and compliant design, implementation, monitoring, and enforcement of a program of special education services in the United States is the Individualized Education Program (IEP). Although IEPs have been used to document procedural compliance with the Individuals with Disabilities Education Act (IDEA) for individual students, IEPs also provide extensive data that can and should be used by a variety of stakeholders including speech-language pathologists (SLPs), school administrators, and state education agencies to design targeted professional development and collectively improve programs, processes, and outcomes in special education. METHOD: We summarize existing literature on the use of IEP data and describe opportunities to use IEP data to analyze individual student service patterns and SLP practice patterns. Aggregated IEP data also provide a robust view of district-wide and state trends in eligibility rates and least restrictive environment settings. Information on current and potential IEP data uses, reflection questions for substantive compliance, and lessons learned from a large-scale analysis of IEP data are provided. These lessons include potential software adjustments to enhance usability as a data source for substantive compliance; program improvement; and monitoring individual, school-wide, and district-wide outcomes. CONCLUSIONS: IEP data are a rich data source of information that may be used to (a) identify trends; (b) assist schools, districts, and states with ensuring substantive compliance with IDEA; (c) examine service equity and efficacy; (d) identify professional development needs; and (e) identify promising practices and provide opportunities to use real-time data to improve models and address public policy.

Constant time delay to teach reading to students with intellectual disability and autism: a review.

The ability to read promotes academic success and serves as an essential prerequisite skill for many postsecondary opportunities. However, developing proficient reading skills is particularly difficult for many individuals with intellectual disability (ID) and autism spectrum disorder (ASD). Reading is an important life skill for all individuals, and it is essential for reading instruction to be grounded in research to achieve optimal learning outcomes. We conducted a review of the literature covering a 15-year period (2005-2020) to examine research measuring the effects of an evidence-based practice, constant time delay (CTD), when used as a reading intervention to teach participants with ID and/or ASD. Studies evaluated the acquisition of functional or academic reading skills across two instructional delivery methods: teacher-delivered and technology-based CTD. All reviewed research used a single case research design to experimentally validate the effects of CTD as a reading intervention, and findings across studies revealed a functional relationship between variables. That is, when applied as a reading intervention, CTD led to acquisition of academic or functional reading skills in participants with ID and/or ASD regardless of delivery method. Recommendations for research and practical application of CTD when teaching reading are provided.

Predicting Language Performance From Narrative Language Samples.

PURPOSE: Analysis of narrative language samples is a recommended clinical practice in the assessment of children's language skills, but we know little about how results from such analyses relate to overall oral language ability across the early school years. We examined the relations between language sample metrics from a short narrative retell, collected in kindergarten, and an oral language factor in grades kindergarten through 3. Our specific questions were to determine the extent to which metrics from narrative language sample analysis are concurrently related to language in kindergarten and predict language through Grade 3. METHOD: Participants were a sample of 284 children who were administered a narrative retell task in kindergarten and a battery of vocabulary and grammar measures in kindergarten through Grade 3. Language samples were analyzed for number of different words, mean length of utterance, and a relatively new metric, percent grammatical utterances (PGUs). Structural equation models were used to estimate the concurrent and longitudinal relationships. RESULTS: The narrative language sample metrics were consistently correlated with the individual vocabulary and grammar measures as well as the language factor in each grade, and also consistently and uniquely predicted the language factor in each grade. Standardized path estimates in the structural equation models ranged from 0.20 to 0.39. CONCLUSIONS: This study found narrative language sample metrics to be predictive, concurrently and longitudinally, of a latent factor of language from kindergarten through Grade 3. These results further validate the importance of collecting and analyzing narrative language samples, to include PGU along with more traditional metrics, and point to directions for future research. SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.17700980.

Metastatic transitional cell carcinoma in proximal humerus of a dog.

Transitional cell carcinoma (TCC) was diagnosed in the proximal humerus of a dog that was presented with persistent right forelimb lameness with no clinical signs of urinary tract involvement. A diagnosis of TCC was made from surgical biopsy of the humeral lesion with subsequent necropsy revealing the prostatic urethra as the primary site of the tumor.

Heterologous expression of the oxytetracycline biosynthetic pathway in Myxococcus xanthus.

New natural products for drug discovery may be accessed by heterologous expression of bacterial biosynthetic pathways in metagenomic DNA libraries. However, a "universal" host is needed for this experiment. Herein, we show that Myxococcus xanthus is a potential "universal" host for heterologous expression of polyketide biosynthetic gene clusters.

Collecting Words: A Clinical Example of a Morphology-Focused Orthographic Intervention.

Purpose Morphological interventions promote gains in morphological knowledge and in other oral and written language skills (e.g., phonological awareness, vocabulary, reading, and spelling), yet we have a limited understanding of critical intervention features. In this clinical focus article, we describe a relatively novel approach to teaching morphology that considers its role as the key organizing principle of English orthography. We also present a clinical example of such an intervention delivered during a summer camp at a university speech and hearing clinic. Method Graduate speech-language pathology students provided a 6-week morphology-focused orthographic intervention to children in first through fourth grade (n = 10) who demonstrated word-level reading and spelling difficulties. The intervention focused children's attention on morphological families, teaching how morphology is interrelated with phonology and etymology in English orthography. Results Comparing pre- and posttest scores, children demonstrated improvement in reading and/or spelling abilities, with the largest gains observed in spelling affixes within polymorphemic words. Children and their caregivers reacted positively to the intervention. Therefore, data from the camp offer preliminary support for teaching morphology within the context of written words, and the intervention appears to be a feasible approach for simultaneously increasing morphological knowledge, reading, and spelling. Conclusion Children with word-level reading and spelling difficulties may benefit from a morphology-focused orthographic intervention, such as the one described here. Research on the approach is warranted, and clinicians are encouraged to explore its possible effectiveness in their practice. Supplemental Material https://doi.org/10.23641/asha.12290687.

Lexical-Level Predictors of Reading Comprehension in Third Grade: Is Spelling a Unique Contributor?

Purpose Considerable research effort has focused on understanding reading comprehension and reading comprehension difficulties. The purpose of this correlational study was to add to the small but growing body of literature on the role that spelling may play in reading comprehension, by investigating the full range of lexical-level literacy skills and whether spelling makes a unique contribution. This study also explored whether these relations vary with the spelling scoring metric. Method Data were collected from 63 children attending Grade 3 in a Midwestern state. In addition to measuring reading comprehension, word recognition, and vocabulary, 4 spelling scoring metrics were examined: the number of words spelled correctly, the number of correct letter sequences (CLS), and Spelling Sensitivity Scores for elements and for words. Results All spelling metrics were significantly correlated with reading comprehension. Results of hierarchical regressions showed that spelling was a significant, unique predictor of reading comprehension when the CLS metric was used. The scoring metrics were differentially related to reading comprehension. Metrics that gave credit based on orthographic precision only (number of words spelled correctly and CLS) were more highly related to reading comprehension than metrics that scored not only on orthographic accuracy but also on phonological and morphological accuracy (Spelling Sensitivity Scores for elements and for words). Conclusion These results indicate that spelling is related to reading comprehension and have theoretical and clinical implications for the use of spelling assessment. Supplemental Material https://doi.org/10.23641/asha.9947216.

Evaluation of lung lobe torsion in Pugs: 7 cases (1991-2004).

OBJECTIVE: To determine whether there is a predis-position for lung lobe torsion (LLT) in Pugs and describe clinical findings associated with LLT in that breed, compared with findings in other breeds. DESIGN: Retrospective case series. ANIMALS: 7 Pugs and 16 dogs of other breeds. PROCEDURE: Information collected from records included signalment, history, lung lobe affected, results of clinicopathologic testing, histologic findings, diagnostic imaging results, surgical treatment, and outcome. RESULTS: 23 dogs were diagnosed with LLT, 10 of which were large-breed dogs and 13 of which were small-breed dogs. Seven of the small-breed dogs were Pugs. Pugs with LLT were significantly overrepresented, compared with the general hospital population. Affected Pugs ranged in age from 4.5 months to 4 years (median, 1.5 years). Six of the 7 Pugs had no predisposing conditions, and 6 were male. Six Pugs survived to discharge. Of the other small- and large-breed dogs, 3 of 6 and 5 of 10 survived to discharge, respectively. None of the Pugs were readmitted for complications or recurrence. CONCLUSIONS AND CLINICAL RELEVANCE: Results indicated that young male Pugs may be predisposed to developing spontaneous LLT. The prognosis for survival and resolution of clinical signs in Pugs with LLT appeared to be excellent. Factors contributing to the development of LLT in Pugs are not known.

Ten Steps to Conducting a Large, Multi-Site, Longitudinal Investigation of Language and Reading in Young Children.

PURPOSE: This paper describes methodological procedures involving execution of a large-scale, multi-site longitudinal study of language and reading comprehension in young children. Researchers in the Language and Reading Research Consortium (LARRC) developed and implemented these procedures to ensure data integrity across multiple sites, schools, and grades. Specifically, major features of our approach, as well as lessons learned, are summarized in 10 steps essential for successful completion of a large-scale longitudinal investigation in early grades. METHOD: Over 5 years, children in preschool through third grade were administered a battery of 35 higher- and lower-level language, listening, and reading comprehension measures (RCM). Data were collected from children, their teachers, and their parents/guardians at four sites across the United States. Substantial and rigorous effort was aimed toward maintaining consistency in processes and data management across sites for children, assessors, and staff. CONCLUSION: With appropriate planning, flexibility, and communication strategies in place, LARRC developed and executed a successful multi-site longitudinal research study that will meet its goal of investigating the contribution and role of language skills in the development of children's listening and reading comprehension. Through dissemination of our design strategies and lessons learned, research teams embarking on similar endeavors can be better equipped to anticipate the challenges.

Understanding Risk for Reading Difficulties in Children With Language Impairment.

Purpose: The purpose of this study was to retrospectively examine the preschool language and early literacy skills of kindergarten good and poor readers, and to determine the extent to which these skills predict reading status. Method: Participants were 136 children with language impairment enrolled in early childhood special education classrooms. On the basis of performance on a word recognition task given in kindergarten, children were classified as either good or poor readers. Comparisons were made across these 2 groups on a number of language and early literacy measures administered in preschool, and logistic regression was used to determine the best predictors of kindergarten reading status. Results: Twenty-seven percent of the sample met criterion for poor reading in kindergarten. These children differed from good readers on most of the skills measured in preschool. The best predictors of kindergarten reading status were oral language, alphabet knowledge, and print concept knowledge. Presence of comorbid disabilities was not a significant predictor. Classification accuracy was good overall. Conclusion: Results suggest that risk of reading difficulty for children with language impairment can be reliably estimated in preschool, prior to the onset of formal reading instruction. Measures of both language and early literacy skills are important for identifying which children are likely to develop later reading difficulties.

The functional status of paraveinal mesophyll vacuoles changes in response to altered metabolic conditions in soybean leaves.

Antibodies raised against tonoplast intrinsic proteins (TIPs) were used to probe the functional status of the soybean [Glycine max (L.) Merr.] paraveinal mesophyll (PVM) vacuole during changes in nitrogen metabolism within the leaf. Young plants grown under standard conditions had PVM vacuoles characterised by the presence of γ-TIP, which is indicative of a lytic function. When plants were then subjected to shoot tip removal for a period of 15 d, forcing a sink-limited physiological condition, the γ-TIP marker diminished while the δ-TIP marker became present in the PVM vacuole, indicating the conversion of the PVM vacuole to a storage function. When the shoot tips were allowed to regrow, the γ-TIP marker again became dominant demonstrating the reversion of these PVM vacuoles back to a lytic compartment. The changes in TIP markers correlated with the accumulation of vegetative storage proteins and vegetative lipoxygenases, proteins implicated in nitrogen storage and assimilate partitioning. This research suggests that the PVM vacuole is able to undergo dynamic conversion between lytic and storage functions and further implicates this cell layer in assimilate storage and mobilisation in soybeans.