Tubular CPT1A deletion minimally affects aging and chronic kidney injury.

Kidney tubules use fatty acid oxidation (FAO) to support their high energetic requirements. Carnitine palmitoyltransferase 1A (CPT1A) is the rate-limiting enzyme for FAO, and it is necessary to transport long-chain fatty acids into mitochondria. To define the role of tubular CPT1A in aging and injury, we generated mice with tubule-specific deletion of Cpt1a (Cpt1aCKO mice), and the mice were either aged for 2 years or injured by aristolochic acid or unilateral ureteral obstruction. Surprisingly, Cpt1aCKO mice had no significant differences in kidney function or fibrosis compared with wild-type mice after aging or chronic injury. Primary tubule cells from aged Cpt1aCKO mice had a modest decrease in palmitate oxidation but retained the ability to metabolize long-chain fatty acids. Very-long-chain fatty acids, exclusively oxidized by peroxisomes, were reduced in kidneys lacking tubular CPT1A, consistent with increased peroxisomal activity. Single-nuclear RNA-Seq showed significantly increased expression of peroxisomal FAO enzymes in proximal tubules of mice lacking tubular CPT1A. These data suggest that peroxisomal FAO may compensate in the absence of CPT1A, and future genetic studies are needed to confirm the role of peroxisomal ß-oxidation when mitochondrial FAO is impaired.

NAD+ precursors and bile acid sequestration treat preclinical refractory environmental enteric dysfunction.

Environmental enteric dysfunction (EED) is a diffuse small bowel disorder associated with poor growth, inadequate responses to oral vaccines, and nutrient malabsorption in millions of children worldwide. We identify loss of the small intestinal Paneth and goblet cells that are critical for innate immunity, reduced villous height, increased bile acids, and dysregulated nicotinamide adenine dinucleotide (NAD+) synthesis signaling as potential mechanisms underlying EED and which also correlated with diminished length-for-age z score. Isocaloric low-protein diet (LPD) consumption in mice recapitulated EED histopathology and transcriptomic changes in a microbiota-independent manner, as well as increases in serum and fecal bile acids. Children with refractory EED harbor single-nucleotide polymorphisms in key enzymes involved in NAD+ synthesis. In mice, deletion of Nampt, the gene encoding the rate-limiting enzyme in the NAD+ salvage pathway, from intestinal epithelium also reduced Paneth cell function, a deficiency that was further aggravated by LPD. Separate supplementation with NAD+ precursors or bile acid sequestrant partially restored LPD-associated Paneth cell defects and, when combined, fully restored all histopathology defects in LPD-fed mice. Therapeutic regimens that increase protein and NAD+ contents while reducing excessive bile acids may benefit children with refractory EED.

Using IRTree Models to Promote Selection Validity in the Presence of Extreme Response Styles.

The measurement of psychological constructs is frequently based on self-report tests, which often have Likert-type items rated from "Strongly Disagree" to "Strongly Agree". Recently, a family of item response theory (IRT) models called IRTree models have emerged that can parse out content traits (e.g., personality traits) from noise traits (e.g., response styles). In this study, we compare the selection validity and adverse impact consequences of noise traits on selection when scores are estimated using a generalized partial credit model (GPCM) or an IRTree model. First, we present a simulation which demonstrates that when noise traits do exist, the selection decisions made based on the IRTree model estimated scores have higher accuracy rates and have less instances of adverse impact based on extreme response style group membership when compared to the GPCM. Both models performed similarly when there was no influence of noise traits on the responses. Second, we present an application using data collected from the Open-Source Psychometrics Project Fisher Temperament Inventory dataset. We found that the IRTree model had a better fit, but a high agreement rate between the model decisions resulted in virtually identical impact ratios between the models. We offer considerations for applications of the IRTree model and future directions for research.

Blocking cell cycle progression through CDK4/6 protects against chronic kidney disease.

Acute and chronic kidney injuries induce increased cell cycle progression in renal tubules. While increased cell cycle progression promotes repair after acute injury, the role of ongoing tubular cell cycle progression in chronic kidney disease is unknown. Two weeks after initiation of chronic kidney disease, we blocked cell cycle progression at G1/S phase by using an FDA-approved, selective inhibitor of CDK4/6. Blocking CDK4/6 improved renal function and reduced tubular injury and fibrosis in 2 murine models of chronic kidney disease. However, selective deletion of cyclin D1, which complexes with CDK4/6 to promote cell cycle progression, paradoxically increased tubular injury. Expression quantitative trait loci (eQTLs) for CCND1 (cyclin D1) and the CDK4/6 inhibitor CDKN2B were associated with eGFR in genome-wide association studies. Consistent with the preclinical studies, reduced expression of CDKN2B correlated with lower eGFR values, and higher levels of CCND1 correlated with higher eGFR values. CDK4/6 inhibition promoted tubular cell survival, in part, through a STAT3/IL-1ß pathway and was dependent upon on its effects on the cell cycle. Our data challenge the paradigm that tubular cell cycle progression is beneficial in the context of chronic kidney injury. Unlike the reparative role of cell cycle progression following acute kidney injury, these data suggest that blocking cell cycle progression by inhibiting CDK4/6, but not cyclin D1, protects against chronic kidney injury.

The Backup Planning Scale (BUPS): A Brief, Self-Reported Measure of a Person's Tendency to Develop, Reserve, and Use Backup Plans.

To mitigate uncertainty in their goal pursuits, people use backup plans, i.e., alternative means that are developed to potentially replace "Plan A." Several studies have demonstrated that backup plans can introduce unexpected costs into goal pursuits that decrease a person's motivation to continue using their "Plan A," and reduce their chances for achieving their goal. These existing studies used time-intensive experimental and/or observational approaches to assess the effects of backup planning. The present research examines the newly-developed Backup Planning Scale (BUPS) for its measurement invariance, reliability, validity, and other psychometric characteristics across three independent samples with more than 1,500 participants. Consistent with prior theorizing, we found support for a nine-item, three factor structure for the BUPS, indexing latent factors for a person's tendency to develop, reserve, and replace with (or use) backup plans. Furthermore, a novel "IRTree" based statistical technique provided evidence for the validity of the measure, as participants' responses to the BUPS were associated with their actual developing, reserving, and replacing backup planning behaviors in a logic task. We conclude that the freely-available BUPS is a simple, brief, reliable, and valid self-reported instrument for assessing backup planning behaviors across adulthood.

Using a Response Time-Based Expected A Posteriori Estimator to Control for Differential Speededness in Computerized Adaptive Test.

This study investigates using response times (RTs) with item responses in a computerized adaptive test (CAT) setting to enhance item selection and ability estimation and control for differential speededness. Using van der Linden's hierarchical framework, an extended procedure for joint estimation of ability and speed parameters for use in CAT is developed following van der Linden; this is called the joint expected a posteriori estimator (J-EAP). It is shown that the J-EAP estimate of ability and speededness outperforms the standard maximum likelihood estimator (MLE) of ability and speededness in terms of correlation, root mean square error, and bias. It is further shown that under the maximum information per time unit item selection method (MICT)-a method which uses estimates for ability and speededness directly-using the J-EAP further reduces average examinee time spent and variability in test times between examinees above the resulting gains of this selection algorithm with the MLE while maintaining estimation efficiency. Simulated test results are further corroborated with test parameters derived from a real data example.

Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation.

Intestinal Paneth cells modulate innate immunity and infection. In Crohn's disease, genetic mutations together with environmental triggers can disable Paneth cell function. Here, we find that a western diet (WD) similarly leads to Paneth cell dysfunction through mechanisms dependent on the microbiome and farnesoid X receptor (FXR) and type I interferon (IFN) signaling. Analysis of multiple human cohorts suggests that obesity is associated with Paneth cell dysfunction. In mouse models, consumption of a WD for as little as 4 weeks led to Paneth cell dysfunction. WD consumption in conjunction with Clostridium spp. increased the secondary bile acid deoxycholic acid levels in the ileum, which in turn inhibited Paneth cell function. The process required excess signaling of both FXR and IFN within intestinal epithelial cells. Our findings provide a mechanistic link between poor diet and inhibition of gut innate immunity and uncover an effect of FXR activation in gut inflammation.

Debaryomyces is enriched in Crohn's disease intestinal tissue and impairs healing in mice.

Alterations of the mycobiota composition associated with Crohn's disease (CD) are challenging to link to defining elements of pathophysiology, such as poor injury repair. Using culture-dependent and -independent methods, we discovered that Debaryomyces hansenii preferentially localized to and was abundant within incompletely healed intestinal wounds of mice and inflamed mucosal tissues of CD human subjects. D. hansenii cultures from injured mice and inflamed CD tissues impaired colonic healing when introduced into injured conventionally raised or gnotobiotic mice. We reisolated D. hansenii from injured areas of these mice, fulfilling Koch's postulates. Mechanistically, D. hansenii impaired mucosal healing through the myeloid cell-specific type 1 interferon-CCL5 axis. Taken together, we have identified a fungus that inhabits inflamed CD tissue and can lead to dysregulated mucosal healing.

A Restricted Four-Parameter IRT Model: The Dyad Four-Parameter Normal Ogive (Dyad-4PNO) Model.

Recently, there has been a renewed interest in the four-parameter item response theory model as a way to capture guessing and slipping behaviors in responses. Research has shown, however, that the nested three-parameter model suffers from issues of unidentifiability (San Martín et al. in Psychometrika 80:450-467, 2015), which places concern on the identifiability of the four-parameter model. Borrowing from recent advances in the identification of cognitive diagnostic models, in particular, the DINA model (Gu and Xu in Stat Sin https://doi.org/10.5705/ss.202018.0420 , 2019), a new model is proposed with restrictions inspired by this new literature to help with the identification issue. Specifically, we show conditions under which the four-parameter model is strictly and generically identified. These conditions inform the presentation of a new exploratory model, which we call the dyad four-parameter normal ogive (Dyad-4PNO) model. This model is developed by placing a hierarchical structure on the DINA model and imposing equality constraints on a priori unknown dyads of items. We present a Bayesian formulation of this model, and show that model parameters can be accurately recovered. Finally, we apply the model to a real dataset.

IRTBEMM: An R Package for Estimating IRT Models With Guessing or Slipping Parameters.

A recently released R package IRTBEMM is presented in this article. This package puts together several new estimation algorithms (Bayesian EMM, Bayesian E3M, and their maximum likelihood versions) for the Item Response Theory (IRT) models with guessing and slipping parameters (e.g., 3PL, 4PL, 1PL-G, and 1PL-AG models). IRTBEMM should be of interest to the researchers in IRT estimation and applying IRT models with the guessing and slipping effects to real datasets.

Autophagy proteins are required for club cell structure and function in airways.

Epithelial cells that line lung airways produce and secrete proteins with important roles in barrier function and host defense. Secretion of airway goblet cells is controlled by autophagy proteins during inflammatory conditions, resulting in accumulation of mucin proteins. We hypothesized that autophagy proteins would also be important in the function of club cells, dominant secretory airway epithelial cells that are dysregulated in chronic lung disease. We found that in the absence of an inflammatory stimulus, mice with club cells deficient for the autophagy protein Atg5 had a markedly diminished expression of secreted host defense proteins secretoglobulin family 1A, member 1 (Scgb1a1) and surfactant proteins A1 and D (Sftpa1 and Sftpd), as well as abnormal club cell morphology. Adult mice with targeted loss of Atg5 also showed diminished levels of host defense proteins in regenerating cells following ablation with naphthalene. A mouse strain with global deficiency of Atg16-like 1 (Atg16l1), an Atg5 binding partner, had a similar loss of host defense proteins and abnormal club cell morphology. Cigarette smoke exposure reduced levels of Scgb1a1 in wild-type mice as expected. Smoke exposure was not required to trigger club cell abnormalities in mice bearing the human ATG16 variant Atg16l1T300A/T300A, which had low Scgb1a1 levels independent of this environmental stress. Evaluation of lung tissues from former smokers with severe chronic obstructive pulmonary disease showed evidence of reduced autophagy and SCGB1A1 expression in club cells. Thus, autophagy proteins are required for the function of club cells, independent of the cellular stress of cigarette smoke, with roles that appear to be distinct from those of other secretory cell types.

High-Stakes Testing Case Study: A Latent Variable Approach for Assessing Measurement and Prediction Invariance.

The existence of differences in prediction systems involving test scores across demographic groups continues to be a thorny and unresolved scientific, professional, and societal concern. Our case study uses a two-stage least squares (2SLS) estimator to jointly assess measurement invariance and prediction invariance in high-stakes testing. So, we examined differences across groups based on latent as opposed to observed scores with data for 176 colleges and universities from The College Board. Results showed that evidence regarding measurement invariance was rejected for the SAT mathematics (SAT-M) subtest at the 0.01 level for 74.5% and 29.9% of cohorts for Black versus White and Hispanic versus White comparisons, respectively. Also, on average, Black students with the same standing on a common factor had observed SAT-M scores that were nearly a third of a standard deviation lower than for comparable Whites. We also found evidence that group differences in SAT-M measurement intercepts may partly explain the well-known finding of observed differences in prediction intercepts. Additionally, results provided evidence that nearly a quarter of the statistically significant observed intercept differences were not statistically significant at the 0.05 level once predictor measurement error was accounted for using the 2SLS procedure. Our joint measurement and prediction invariance approach based on latent scores opens the door to a new high-stakes testing research agenda whose goal is to not simply assess whether observed group-based differences exist and the size and direction of such differences. Rather, the goal of this research agenda is to assess the causal chain starting with underlying theoretical mechanisms (e.g., contextual factors, differences in latent predictor scores) that affect the size and direction of any observed differences.

Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn's disease.

It is suggested that subtyping of complex inflammatory diseases can be based on genetic susceptibility and relevant environmental exposure (G+E). We propose that using matched cellular phenotypes in human subjects and corresponding preclinical models with the same G+E combinations is useful to this end. As an example, defective Paneth cells can subtype Crohn's disease (CD) subjects; Paneth cell defects have been linked to multiple CD susceptibility genes and are associated with poor outcome. We hypothesized that CD susceptibility genes interact with cigarette smoking, a major CD environmental risk factor, to trigger Paneth cell defects. We found that both CD subjects and mice with ATG16L1T300A (T300A; a prevalent CD susceptibility allele) developed Paneth cell defects triggered by tobacco smoke. Transcriptional analysis of full-thickness ileum and Paneth cell-enriched crypt base cells showed the T300A-smoking combination altered distinct pathways, including proapoptosis, metabolic dysregulation, and selective downregulation of the PPARγ pathway. Pharmacologic intervention by either apoptosis inhibitor or PPARγ agonist rosiglitazone prevented smoking-induced crypt apoptosis and Paneth cell defects in T300A mice and mice with conditional Paneth cell-specific knockout of Atg16l1. This study demonstrates how explicit G+E can drive disease-relevant phenotype and provides rational strategies for identifying actionable targets.

The role of multiple-group measurement invariance in family psychology research.

Measurement invariance (MI) is a property of measurement that is often implicitly assumed, but in many cases, not tested. When the assumption of MI is tested, it generally involves determining if the measurement holds longitudinally or cross-culturally. A growing literature shows that other groupings can, and should, be considered as well. Additionally, it is noted that the standard techniques for investigating MI have been focused almost exclusively on the case of 2 groups, with very little work on the case of more than 2 groups, even though the need for such techniques is apparent in many fields of research. This paper introduces and illustrates a model building technique to investigating MI for more than 2 groups. This technique is an extension of the already-existing hierarchy for testing MI introduced by Meredith (1993). An example using data on father involvement in 5 different groups of families of children with and without developmental disabilities from the Early Childhood Longitudinal Study-Birth Cohort dataset will be given. We show that without considering the possible differential functioning of the measurements on multiple developmental groups, the differences present between the groups in terms of the measurements may be obscured. This could lead to incorrect conclusions.

Father involvement and maternal depressive symptoms in families of children with disabilities or delays.

This study examined the longitudinal association between fathers' early involvement in routine caregiving, literacy, play, and responsive caregiving activities at 9 months and maternal depressive symptoms at 4 years. Data for 3,550 children and their biological parents were drawn from the Early Childhood Longitudinal Study-Birth Cohort data set. Analyses in a structural equation modeling framework examined whether the association between father involvement and maternal depressive symptoms differed for families of children with autism spectrum disorder (ASD) and for families of children with other disabilities or delays from families of children who were typically developing. Results indicated that father literacy and responsive caregiving involvement were associated with lower levels of depressive symptoms for mothers of children with ASD. These findings indicate that greater father involvement may benefit families of children with ASD and highlight the need to support and encourage service providers to work with fathers.

Branched signal wiring of an essential bacterial cell-cycle phosphotransfer protein.

Vital to bacterial survival is the faithful propagation of cellular signals, and in Caulobacter crescentus, ChpT is an essential mediator within the cell-cycle circuit. ChpT functions as a histidine-containing phosphotransfer protein (HPt) that shuttles a phosphoryl group from the receiver domain of CckA, the upstream hybrid histidine kinase (HK), to one of two downstream response regulators (CtrA or CpdR) that controls cell-cycle progression. To understand how ChpT interacts with multiple signaling partners, we solved the crystal structure of ChpT at 2.3 Å resolution. ChpT adopts a pseudo-HK architecture but does not bind ATP. We identified two point mutation classes affecting phosphotransfer and cell morphology: one that globally impairs ChpT phosphotransfer, and a second that mediates partner selection. Importantly, a small set of conserved ChpT residues promotes signaling crosstalk and contributes to the branched signaling that activates the master regulator CtrA while inactivating the CtrA degradation signal, CpdR.

Synthesis of lipoteichoic acids in Bacillus anthracis.

Lipoteichoic acid (LTA), a glycerol phosphate polymer, is a component of the envelope of Gram-positive bacteria that has hitherto not been identified in Bacillus anthracis, the causative agent of anthrax. LTA synthesis in Staphylococcus aureus and other microbes is catalyzed by the product of the ltaS gene, a membrane protein that polymerizes polyglycerol phosphate from phosphatidyl glycerol. Here we identified four ltaS homologues, designated ltaS1 to -4, in the genome of Bacillus anthracis. Polyglycerol phosphate-specific monoclonal antibodies were used to detect LTA in the envelope of B. anthracis strain Sterne (pXO1(+) pXO2(-)) vegetative forms. B. anthracis mutants lacking ltaS1, ltaS2, ltaS3, or ltaS4 did not display defects in growth or LTA synthesis. In contrast, B. anthracis strains lacking both ltaS1 and ltaS2 were unable to synthesize LTA and exhibited reduced viability, altered envelope morphology, aberrant separation of vegetative forms, and decreased sporulation efficiency. Expression of ltaS1 or ltaS2 alone in B. anthracis as well as in other microbes was sufficient for polyglycerol phosphate synthesis. Thus, similar to S. aureus, B. anthracis employs LtaS enzymes to synthesize LTA, an envelope component that promotes bacterial growth and cell division.

Surface-layer (S-layer) proteins sap and EA1 govern the binding of the S-layer-associated protein BslO at the cell septa of Bacillus anthracis.

The Gram-positive pathogen Bacillus anthracis contains 24 genes whose products harbor the structurally conserved surface-layer (S-layer) homology (SLH) domain. Proteins endowed with the SLH domain associate with the secondary cell wall polysaccharide (SCWP) following secretion. Two such proteins, Sap and EA1, have the unique ability to self-assemble into a paracrystalline layer on the surface of bacilli and form S layers. Other SLH domain proteins can also be found within the S layer and have been designated Bacillus S-layer-associated protein (BSLs). While both S-layer proteins and BSLs bind the same SCWP, their deposition on the cell surface is not random. For example, BslO is targeted to septal peptidoglycan zones, where it catalyzes the separation of daughter cells. Here we show that an insertional lesion in the sap structural gene results in elongated chains of bacilli, as observed with a bslO mutant. The chain length of the sap mutant can be reduced by the addition of purified BslO in the culture medium. This complementation in trans can be explained by an increased deposition of BslO onto the surface of sap mutant bacilli that extends beyond chain septa. Using fluorescence microscopy, we observed that the Sap S layer does not overlap the EA1 S layer and slowly yields to the EA1 S layer in a growth-phase-dependent manner. Although present all over bacilli, Sap S-layer patches are not observed at septa. Thus, we propose that the dynamic Sap/EA1 S-layer coverage of the envelope restricts the deposition of BslO to the SCWP at septal rings.

The SLH-domain protein BslO is a determinant of Bacillus anthracis chain length.

The Gram-positive pathogen Bacillus anthracis grows in characteristic chains of individual, rod-shaped cells. Here, we report the cell-separating activity of BslO, a putative N-acetylglucosaminidase bearing three N-terminal S-layer homology (SLH) domains for association with the secondary cell wall polysaccharide (SCWP). Mutants with an insertional lesion in the bslO gene exhibit exaggerated chain lengths, although individual cell dimensions are unchanged. Purified BslO complements this phenotype in trans, effectively dispersing chains of bslO-deficient bacilli without lysis and localizing to the septa of vegetative cells. Compared with the extremely long chain lengths of csaB bacilli, which are incapable of binding proteins with SLH-domains to SCWP, bslO mutants demonstrate a chaining phenotype that is intermediate between wild-type and csaB. Computational simulation suggests that BslO effects a non-random distribution of B. anthracis chain lengths, implying that all septa are not equal candidates for separation.

Structure of surface layer homology (SLH) domains from Bacillus anthracis surface array protein.

Surface (S)-layers, para-crystalline arrays of protein, are deposited in the envelope of most bacterial species. These surface organelles are retained in the bacterial envelope through the non-covalent association of proteins with cell wall carbohydrates. Bacillus anthracis, a Gram-positive pathogen, produces S-layers of the protein Sap, which uses three consecutive repeats of the surface-layer homology (SLH) domain to engage secondary cell wall polysaccharides (SCWP). Using x-ray crystallography, we reveal here the structure of these SLH domains, which assume the shape of a three-prong spindle. Each SLH domain contributes to a three-helical bundle at the spindle base, whereas another α-helix and its connecting loops generate the three prongs. The inter-prong grooves contain conserved cationic and anionic residues, which are necessary for SLH domains to bind the B. anthracis SCWP. Modeling experiments suggest that the SLH domains of other S-layer proteins also fold into three-prong spindles and capture bacterial envelope carbohydrates by a similar mechanism.