Community Culture Survey - Revised: Measuring neighborhood culture and exploring geographic, socioeconomic, and cultural determinants of health in samples across the United States and in Thailand.

Objectives: Research on links between social, geographic, and cultural determinants of health has been thwarted by inadequate measures of culture. The purpose of this study was to improve the measurement of community culture, defined as shared patterns of attitudes and behaviors among people within a neighborhood that distinguish it from others, and to examine dimensions of culture, independent of socioeconomic and demographic factors, and their relationships with health. Study design: A survey research design with correlational analyses was used. Methods: A survey packet including the Community Culture Survey - Revised (CCS-R), demographic, health, and other individual-level measures was administered through convenience sampling across the United States (US) and to a sample in Thailand from 2016 to 2018. US county-level variables were obtained from zip codes. Results: 1930 participants from 49 US states (n = 1592) and Thailand (n = 338) completed all CCS-R items, from which 12 subscales were derived: Social Support & Connectedness, Responsibility for Self & Others, Family Ties & Duties, Social Distress, Urban Diversity, Discontinuity, Church-Engaged, External Resource-Seeking, Locally Owned Business-Active, Power Deference, Next Generation Focus, and Self-Reliance. Neighborhood culture subscale scores varied more by geography than by participant's demographics. All subscales predicted one or more health indicator, and some of these relationships were significant after adjusting for participant age and county-level socioeconomic variables. Most of the significant differences on subscales by race/ethnicity were no longer significant after adjusting for participant's age and county-level socioeconomic variables. Most rural/urban and regional differences in culture within the US persisted after these adjustments. Based on correlational analyses, Social Support & Connectedness and Responsibility for Self & Others were the best predictors of participants' overall health and quality of life, and Responsibility for Self & Others was the best predictor (inversely) of the CDC's measures of social vulnerability. Conclusions: Neighborhood culture is measurable, multi-dimensional, distinct from race/ethnicity, and related to health even after controlling for age and socioeconomic factors. The CCS-R is useful for advancing research and practice addressing the complex interactions between individuals, their neighborhood communities, and health outcomes.

SUB-Immunogold-SEM reveals nanoscale distribution of submembranous epitopes.

Electron microscopy paired with immunogold labeling is the most precise tool for protein localization. However, these methods are either cumbersome, resulting in small sample numbers and restricted quantification, or limited to identifying protein epitopes external to the membrane. Here, we introduce SUB-immunogold-SEM, a scanning electron microscopy technique that detects intracellular protein epitopes proximal to the membrane. We identified four critical sample preparation factors that contribute to the method's sensitivity and validate its efficacy through precise localization and high-powered quantification of cytoskeletal and transmembrane proteins. We evaluated the capabilities of SUB-immunogold-SEM on cells with highly differentiated apical surfaces: (i) auditory hair cells, revealing the presence of nanoscale Myosin rings at the tip of stereocilia; and (ii) respiratory multiciliate cells, mapping the distribution of the SARS-CoV-2 receptor ACE2 along the motile cilia. SUB-immunogold-SEM provides a novel solution for nanoscale protein localization at the exposed surface of any cell.

LOXHD1 is indispensable for coupling auditory mechanosensitive channels to the site of force transmission.

Hearing is initiated in hair cells by the mechanical activation of ion channels in the hair bundle. The hair bundle is formed by stereocilia organized into rows of increasing heights interconnected by tip links, which convey sound-induced forces to stereocilia tips. The auditory mechanosensitive channels are complexes containing at least four protein-subunits - TMC1/2, TMIE, CIB2, and LHFPL51-16 - and are located at the tips of shorter stereocilia at a yet-undetermined distance from the lower tip link insertion point17. While multiple auditory channel subunits appear to interact with the tip link, it remains unknown whether their combined interaction alone can resist the high-frequency mechanical stimulations owing to sound. Here we show that an unanticipated additional element, LOXHD1, is indispensable for maintaining the TMC1 pore-forming channel subunits coupled to the tip link. We demonstrate that LOXHD1 is a unique element of the auditory mechanotransduction complex that selectively affects the localization of TMC1, but not its close developmental paralogue TMC2. Taking advantage of our novel immunogold scanning electron microscopy method for submembranous epitopes (SUB-immunogold-SEM), we demonstrate that TMC1 normally concentrates within 100-nm of the tip link insertion point. In LOXHD1's absence, TMC1 is instead mislocalized away from this force transmission site. Supporting this finding, we found that LOXHD1 interacts selectively in vitro with TMC1 but not with TMC2 while also binding to channel subunits CIB2 and LHFPL5 and tip-link protein PCDH15. SUB-immunogold-SEM additionally demonstrates that LOXHD1 and TMC1 are physically connected to the lower tip-link complex in situ. Our results show that the TMC1-driven mature channels require LOXHD1 to stay coupled to the tip link and remain functional, but the TMC2-driven developmental channels do not. As both tip links and TMC1 remain present in hair bundles lacking LOXHD1, it opens the possibility to reconnect them and restore hearing for this form of genetic deafness.

Climate change-informed dietary modeling in Pacific cod: Experimentally-derived effects of temperature and dietary quality on carbon and nitrogen stable isotope trophic discrimination factors.

Stable isotope analysis is a powerful tool for dietary modeling and trophic ecology research. A crucial piece of information for isotopic dietary modeling is the accurate estimation of trophic discrimination factors (TDFs), or the isotopic offset between a consumer's tissue and its diet. In order to parameterize stable isotope dietary models for future climate scenarios, we investigated the effect of water temperature and dietary protein and lipid content on TDFs in juvenile Pacific cod (Gadus macrocephalus). Pacific cod are a commercially and ecologically important species, with stock numbers in the northeast Pacific recently having dropped by more than 70%. We tested four water temperatures (6, 8, 10, and 12°C) and two dietary regimens (low and high lipid content), representing a range of potential ocean temperature and prey quality scenarios, in order to determine carbon and nitrogen TDFs in juvenile Pacific cod. Additionally, we assessed dietary intake and proximate composition of the experimental fish in order to estimate consumption, assimilation, and retention of dietary nutrients. The results of this study suggest that dietary protein catabolism is a primary driver of nitrogen TDF variability in juvenile Pacific cod. Across all temperature treatments from 6 to 12°C, fish reared on the lower quality, lower lipid content diet had higher nitrogen TDFs. The mean TDFs for fish raised on the higher lipid, lower protein diet were +3.40 ‰ for nitrogen (Δ15N) and +0.36 ‰ for lipid-corrected carbon (Δ LC 13C). The mean TDFs for fish raised on the lower lipid, higher protein diet were +4.09 ‰ for nitrogen (Δ15N) and 0.00 ‰ for lipid-corrected carbon (Δ LC 13C). Lipid-corrected carbon isotope data showed that, regardless of temperature, fish consuming the lower lipid diet had essentially no trophic discrimination between diet and bulk tissues. We found no ecologically meaningful differences in TDFs due to water temperature across the 6°experimental range. The results of this experiment demonstrate that dietary quality, and more specifically the use of dietary protein for energetic needs, is a primary driver of trophic discrimination factors. The TDFs determined in this study can be applied to understanding trophic ecology in Pacific cod and closely related species under rapidly changing prey availability and ocean temperature conditions.

Next-generation sequencing-based MRD in adults with ALL undergoing hematopoietic cell transplantation.

Measurable residual disease (MRD) is an adverse prognostic factor in adult patients with acute lymphoblastic leukemia (ALL) undergoing hematopoietic cell transplant (HCT). Next-generation sequencing (NGS) can detect MRD with a sensitivity of 10-6, but the prognostic value of NGS-based MRD in adult patients with ALL undergoing HCT remains minimally studied. To evaluate the prognostic value of NGS-based MRD in adult patients with ALL undergoing HCT, patients aged ≥18 years with ALL who underwent allogeneic HCT at Stanford University or Oregon Health & Science University between January 2014 and April 2021 and were evaluated for MRD using the NGS-based clonoSEQ assay were included in this study. MRD was assessed before HCT (MRDpre) and up to 1 year after HCT (MRDpost). Patients were followed up for leukemia relapse and survival for up to 2 years after HCT. In total, 158 patients had a trackable clonotype for MRD monitoring. The cumulative incidence of relapse was increased at all levels of MRDpre, including in patients who had low MRDpre of <10-4 (hazard ratio [HR], 3.56; 95% confidence interval [95% CI], 1.39-9.15). In multivariable analysis, MRDpre level remained significantly prognostic; however, detectable MRDpost was the strongest predictor of relapse (HR, 4.60; 95% CI, 3.01-7.02). In exploratory analyses limited to patients with B-cell ALL, the detection of post-HCT immunoglobulin H (IgH) MRD clonotypes, rather than non-IgH MRD clonotypes, was associated with relapse. In this analysis across 2 large transplant centers, we found that the detection of MRD by NGS at a level of 10-6 offers significant prognostic value in adults with ALL undergoing HCT.

Facility-based care for moderately low birthweight infants in India, Malawi, and Tanzania.

Globally, increasing rates of facility-based childbirth enable early intervention for small vulnerable newborns. We describe health system-level inputs, current feeding, and discharge practices for moderately low birthweight (MLBW) infants (1500-<2500g) in resource-constrained settings. The Low Birthweight Infant Feeding Exploration study is a mixed methods observational study in 12 secondary- and tertiary-level facilities in India, Malawi, and Tanzania. We analyzed data from baseline facility assessments and a prospective cohort of 148 MLBW infants from birth to discharge. Anthropometric measuring equipment (e.g., head circumference tapes, length boards), key medications (e.g., surfactant, parenteral nutrition), milk expression tools, and human milk alternatives (e.g., donor milk, formula) were not universally available. MLBW infants were preterm appropriate-for-gestational age (38.5%), preterm large-for-gestational age (3.4%), preterm small-for-gestational age (SGA) (11.5%), and term SGA (46.6%). The median length of stay was 3.1 days (IQR: 1.5, 5.7); 32.4% of infants were NICU-admitted and 67.6% were separated from mothers at least once. Exclusive breastfeeding was high (93.2%). Generalized group lactation support was provided; 81.8% of mother-infant dyads received at least one session and 56.1% had 2+ sessions. At the time of discharge, 5.1% of infants weighed >10% less than their birthweight; 18.8% of infants were discharged with weights below facility-specific policy [1800g in India, 1500g in Malawi, and 2000g in Tanzania]. Based on descriptive analysis, we found constraints in health system inputs which have the potential to hinder high quality care for MLBW infants. Targeted LBW-specific lactation support, discharge at appropriate weight, and access to feeding alternatives would position MLBW for successful feeding and growth post-discharge.

Beyond chest pain: Incremental value of other variables to identify patients for an early ECG.

BACKGROUND: Chest pain (CP) is the hallmark symptom for acute coronary syndrome (ACS) but is not reported in 20-30% of patients, especially women, elderly, non-white patients, presenting to the emergency department (ED) with an ST-segment elevation myocardial infarction (STEMI). METHODS: We used a retrospective 5-year adult ED sample of 279,132 patients to explore using CP alone to predict ACS, then we incrementally added other ACS chief complaints, age, and sex in a series of multivariable logistic regression models. We evaluated each model's identification of ACS and STEMI. RESULTS: Using CP alone would recommend ECGs for 8% of patients (sensitivity, 61%; specificity, 92%) but missed 28.4% of STEMIs. The model with all variables identified ECGs for 22% of patients (sensitivity, 82%; specificity, 78%) but missed 14.7% of STEMIs. The model with CP and other ACS chief complaints had the highest sensitivity (93%) and specificity (55%), identified 45.1% of patients for ECG, and only missed 4.4% of STEMIs. CONCLUSION: CP alone had highest specificity but lacked sensitivity. Adding other ACS chief complaints increased sensitivity but identified 2.2-fold more patients for ECGs. Achieving an ECG in 10 min for patients with ACS to identify all STEMIs will be challenging without introducing more complex risk calculation into clinical care.

Feeding practices and growth patterns of moderately low birthweight infants in resource-limited settings: results from a multisite, longitudinal observational study.

OBJECTIVES: To describe the feeding profile of low birthweight (LBW) infants in the first half of infancy; and to examine growth patterns and early risk factors of poor 6-month growth outcomes. DESIGN: Prospective observational cohort study. SETTING AND PARTICIPANTS: Stable, moderately LBW (1.50 to <2.50 kg) infants were enrolled at birth from 12 secondary/tertiary facilities in India, Malawi and Tanzania and visited nine times over 6 months. VARIABLES OF INTEREST: Key variables of interest included birth weight, LBW type (combination of preterm/term status and size-for-gestational age at birth), lactation practices and support, feeding profile, birthweight regain by 2 weeks of age and poor 6-month growth outcomes. RESULTS: Between 13 September 2019 and 27 January 2021, 1114 infants were enrolled, comprising 4 LBW types. 363 (37.3%) infants initiated early breast feeding and 425 (43.8%) were exclusively breastfed to 6 months. 231 (22.3%) did not regain birthweight by 2 weeks; at 6 months, 280 (32.6%) were stunted, 222 (25.8%) underweight and 88 (10.2%) wasted. Preterm-small-for-gestational age (SGA) infants had 1.89 (95% CI 1.37 to 2.62) and 2.32 (95% CI 1.48 to 3.62) times greater risks of being stunted and underweight at 6 months compared with preterm-appropriate-for-gestational age (AGA) infants. Term-SGA infants had 2.33 (95% CI 1.77 to 3.08), 2.89 (95% CI 1.97 to 4.24) and 1.99 (95% CI 1.13 to 3.51) times higher risks of being stunted, underweight and wasted compared with preterm-AGA infants. Those not regaining their birthweight by 2 weeks had 1.51 (95% CI 1.23 to 1.85) and 1.55 (95% CI 1.21 to 1.99) times greater risks of being stunted and underweight compared with infants regaining. CONCLUSION: LBW type, particularly SGA regardless of preterm or term status, and lack of birthweight regain by 2 weeks are important risk identification parameters. Early interventions are needed that include optimal feeding support, action-oriented growth monitoring and understanding of the needs and growth patterns of SGA infants to enable appropriate weight gain and proactive management of vulnerable infants. TRIAL REGISTRATION NUMBER: NCT04002908.

High-resolution immunofluorescence imaging of mouse cochlear hair bundles.

High-resolution immunofluorescence imaging of cochlear hair bundles faces many challenges due to the hair bundle's small dimensions, fragile nature, and complex organization. Here, we describe an optimized protocol for hair-bundle protein immunostaining and localization. We detail the steps and solutions for extracting and fixing the mouse inner ear and for dissecting the organ of Corti. We further emphasize the optimal permeabilization, blocking, staining, and mounting conditions as well as the parameters for high-resolution microscopy imaging. For complete details on the use and execution of this protocol, please refer to Trouillet et al. (2021).

Dimensions of a Living Cochlear Hair Bundle.

The hair bundle is the mechanosensory organelle of hair cells that detects mechanical stimuli caused by sounds, head motions, and fluid flows. Each hair bundle is an assembly of cellular-protrusions called stereocilia, which differ in height to form a staircase. Stereocilia have different heights, widths, and separations in different species, sensory organs, positions within an organ, hair-cell types, and even within a single hair bundle. The dimensions of the stereociliary assembly dictate how the hair bundle responds to stimuli. These hair-bundle properties have been measured previously only to a limited degree. In particular, mammalian data are either incomplete, lack control for age or position within an organ, or have artifacts owing to fixation or dehydration. Here, we provide a complete set of measurements for postnatal day (P) 11 C57BL/6J mouse apical inner hair cells (IHCs) obtained from living tissue, tissue mildly-fixed for fluorescent imaging, or tissue strongly fixed and dehydrated for scanning electronic microscopy (SEM). We found that hair bundles mildly-fixed for fluorescence had the same dimensions as living hair bundles, whereas SEM-prepared hair bundles shrank uniformly in stereociliary heights, widths, and separations. By determining the shrinkage factors, we imputed live dimensions from SEM that were too small to observe optically. Accordingly, we created the first complete blueprint of a living IHC hair bundle. We show that SEM-prepared measurements strongly affect calculations of a bundle's mechanical properties - overestimating stereociliary deflection stiffness and underestimating the fluid coupling between stereocilia. The methods of measurement, the data, and the consequences we describe illustrate the high levels of accuracy and precision required to understand hair-bundle mechanotransduction.

Impacts of brewing time, brewing temperature and brands on the leaching of phthalates and bisphenol A in dry tea.

Although tea is often considered a healthy drink, there is the possibility for it to contain bisphenol A and phthalates. This project was designed to quantitate the amount of these compounds when tea was prepared in a variety of conditions, and with a variety of different brands and flavours. BPA and phthalates were extracted using solid phase extraction and quantitated using gas chromatography - mass spectrometry. The leaching concentration of di-n-butyl phthalate, a major phthalate in dry tea samples, increased with respect to both brewing time and temperature at rates of 5.9 ng/g/min and 2.3 ng/g/°C, respectively. Loose leaf green teas showed lower concentrations of contaminants than bagged teas. The highest concentrations found of all compounds were for benzylbutyl phthalate in both Brand2 English breakfast and Brand2 green teas with concentrations of 244 ± 76 ng/g and 197 ± 9 ng/g, respectively. Di-n-butyl phthalate, benzylbutyl phthalate and bis-2-ethylhexyl phthalate were all present in concentrations of 50 ng/g or more in 3 or more samples.

Loxhd1 Mutations Cause Mechanotransduction Defects in Cochlear Hair Cells.

Sound detection happens in the inner ear via the mechanical deflection of the hair bundle of cochlear hair cells. The hair bundle is an apical specialization consisting of actin-filled membrane protrusions (called stereocilia) connected by tip links (TLs) that transfer the deflection force to gate the mechanotransduction channels. Here, we identified the hearing loss-associated Loxhd1/DFNB77 gene as being required for the mechanotransduction process. LOXHD1 consists of 15 polycystin lipoxygenase α-toxin (PLAT) repeats, which in other proteins can bind lipids and proteins. LOXHD1 was distributed along the length of the stereocilia. Two LOXHD1 mouse models with mutations in the 10th PLAT repeat exhibited mechanotransduction defects (in both sexes). While mechanotransduction currents in mutant inner hair cells (IHCs) were similar to wild-type levels in the first postnatal week, they were severely affected by postnatal day 11. The onset of the mechanotransduction phenotype was consistent with the temporal progression of postnatal LOXHD1 expression/localization in the hair bundle. The mechanotransduction defect observed in Loxhd1-mutant IHCs was not accompanied by a morphologic defect of the hair bundle or a reduction in TL number. Using immunolocalization, we found that two proteins of the upper and lower TL protein complexes (Harmonin and LHFPL5) were maintained in the mutants, suggesting that the mechanotransduction machinery was present but not activatable. This work identified a novel LOXHD1-dependent step in hair bundle development that is critical for mechanotransduction in mature hair cells as well as for normal hearing function in mice and humans.SIGNIFICANCE STATEMENT Hair cells detect sound-induced forces via the hair bundle, which consists of membrane protrusions connected by tip links. The mechanotransduction machinery forms protein complexes at the tip-link ends. The current study showed that LOXHD1, a multirepeat protein responsible for hearing loss in humans and mice when mutated, was required for hair-cell mechanotransduction, but only after the first postnatal week. Using immunochemistry, we demonstrated that this defect was not caused by the mislocalization of the tip-link complex proteins Harmonin or LHFPL5, suggesting that the mechanotransduction protein complexes were maintained. This work identified a new step in hair bundle development, which is critical for both hair-cell mechanotransduction and hearing.

Bassoon proteinopathy drives neurodegeneration in multiple sclerosis.

Multiple sclerosis (MS) is characterized by inflammatory insults that drive neuroaxonal injury. However, knowledge about neuron-intrinsic responses to inflammation is limited. By leveraging neuron-specific messenger RNA profiling, we found that neuroinflammation leads to induction and toxic accumulation of the synaptic protein bassoon (Bsn) in the neuronal somata of mice and patients with MS. Neuronal overexpression of Bsn in flies resulted in reduction of lifespan, while genetic disruption of Bsn protected mice from inflammation-induced neuroaxonal injury. Notably, pharmacological proteasome activation boosted the clearance of accumulated Bsn and enhanced neuronal survival. Our study demonstrates that neuroinflammation initiates toxic protein accumulation in neuronal somata and advocates proteasome activation as a potential remedy.

TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease.

The RNA-binding protein TDP-43 is heavily implicated in neurodegenerative disease. Numerous patient mutations in TARDBP, the gene encoding TDP-43, combined with data from animal and cell-based models, imply that altered RNA regulation by TDP-43 causes Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. However, underlying mechanisms remain unresolved. Increased cytoplasmic TDP-43 levels in diseased neurons suggest a possible role in this cellular compartment. Here, we examined the impact on translation of overexpressing human TDP-43 and the TDP-43A315T patient mutant protein in motor neuron-like cells and primary cultures of cortical neurons. In motor-neuron like cells, TDP-43 associates with ribosomes without significantly affecting global translation. However, ribosome profiling and additional assays revealed enhanced translation and direct binding of Camta1, Mig12, and Dennd4a mRNAs. Overexpressing either wild-type TDP-43 or TDP-43A315T stimulated translation of Camta1 and Mig12 mRNAs via their 5'UTRs and increased CAMTA1 and MIG12 protein levels. In contrast, translational enhancement of Dennd4a mRNA required a specific 3'UTR region and was specifically observed with the TDP-43A315T patient mutant allele. Our data reveal that TDP-43 can function as an mRNA-specific translational enhancer. Moreover, since CAMTA1 and DENND4A are linked to neurodegeneration, they suggest that this function could contribute to disease.

Thalidomide treatment prevents chronic graft rejection after aortic transplantation in rats - an experimental study.

Cardiac allograft vasculopathy (CAV) affects approximately 30% of cardiac transplant patients at 5 years post-transplantation. To date, there are few CAV treatment or prevention options, none of which are highly effective. The aim of the study was to investigate the effect of thalidomide on the development of CAV. The effect of thalidomide treatment on chronic rejection was assessed in rat orthotopic aortic transplants in allogeneic F344 or syngeneic Lew rats (n = 6 per group). Animals were left untreated or received thalidomide for 30 days post-transplant, and evidence of graft CAV was determined by histology (trichrome and immunohistochemistry) and intragraft cytokine measurements. Animals that received thalidomide treatment post-transplant showed markedly reduced luminal obliteration, with concomitant rescue of smooth muscle cells (SMCs) in the aortic media of grafts. Thalidomide counteracted neointimal hyperplasia by preventing dedifferentiation of vascular SMCs. Measurement of intragraft cytokine levels after thalidomide treatment revealed downregulation of matrix metalloproteinase 8 and monocyte chemotactic protein 1, cytokines involved in tissue remodelling and inflammation, respectively. Importantly, no negative side effects of thalidomide were observed. Thalidomide treatment prevents CAV development in a rodent model and is therefore potentially useful in clinical applications to prevent post-transplant heart rejection.

DENR-MCT-1 promotes translation re-initiation downstream of uORFs to control tissue growth.

During cap-dependent eukaryotic translation initiation, ribosomes scan messenger RNA from the 5' end to the first AUG start codon with favourable sequence context. For many mRNAs this AUG belongs to a short upstream open reading frame (uORF), and translation of the main downstream ORF requires re-initiation, an incompletely understood process. Re-initiation is thought to involve the same factors as standard initiation. It is unknown whether any factors specifically affect translation re-initiation without affecting standard cap-dependent translation. Here we uncover the non-canonical initiation factors density regulated protein (DENR) and multiple copies in T-cell lymphoma-1 (MCT-1; also called MCTS1 in humans) as the first selective regulators of eukaryotic re-initiation. mRNAs containing upstream ORFs with strong Kozak sequences selectively require DENR-MCT-1 for their proper translation, yielding a novel class of mRNAs that can be co-regulated and that is enriched for regulatory proteins such as oncogenic kinases. Collectively, our data reveal that cells have a previously unappreciated translational control system with a key role in supporting proliferation and tissue growth.

A novel mouse model for inhibition of DOHH-mediated hypusine modification reveals a crucial function in embryonic development, proliferation and oncogenic transformation.

The central importance of translational control by post-translational modification has spurred major interest in regulatory pathways that control translation. One such pathway uniquely adds hypusine to eukaryotic initiation factor 5A (eIF5A), and thereby affects protein synthesis and, subsequently, cellular proliferation through an unknown mechanism. Using a novel conditional knockout mouse model and a Caenorhabditis elegans knockout model, we found an evolutionarily conserved role for the DOHH-mediated second step of hypusine synthesis in early embryonic development. At the cellular level, we observed reduced proliferation and induction of senescence in 3T3 Dohh-/- cells as well as reduced capability for malignant transformation. Furthermore, mass spectrometry showed that deletion of DOHH results in an unexpected complete loss of hypusine modification. Our results provide new biological insight into the physiological roles of the second step of the hypusination of eIF5A. Moreover, the conditional mouse model presented here provides a powerful tool for manipulating hypusine modification in a temporal and spatial manner, to analyse both how this unique modification normally functions in vivo as well as how it contributes to different pathological conditions.

Marshalin, a microtubule minus-end binding protein, regulates cytoskeletal structure in the organ of Corti.

Dramatic structural changes in microtubules (MT) and the assembly of complicated intercellular connections are seen during the development of the cellular matrix of the sense organ for hearing, the organ of Corti. This report examines the expression of marshalin, a minus-end binding protein, during this process of cochlear development. We discovered that marshalin is abundantly expressed in both sensory hair cells and supporting cells. In the adult, prominent marshalin expression is observed in the cuticular plates of hair cells and in the noncentrosomal MT organization centers (MTOC) of Deiters' and pillar cells. Based upon differences in marshalin expression patterns seen in the organ of Corti, we identified eight isoforms ranging from 863 to 1280 amino acids. mRNAs/proteins associated with marshalin's isoforms are detected at different times during development. These isoforms carry various protein-protein interacting domains, including coiled-coil (CC), calponin homology (CH), proline-rich (PR), and MT-binding domains, referred to as CKK. We, therefore, examined membranous organelles and structural changes in the cytoskeleton induced by expressing two of these marshalin isoforms in vitro. Long forms containing CC and PR domains induce thick, spindle-shaped bundles, whereas short isoforms lacking CC and PR induce more slender variants that develop into densely woven networks. Together, these data suggest that marshalin is closely associated with noncentrosomal MTOCs, and may be involved in MT bundle formation in supporting cells. As a scaffolding protein with multiple isoforms, marshalin is capable of modifying cytoskeletal networks, and consequently organelle positioning, through interactions with various protein partners present in different cells.

2010 translational bioinformatics year in review.

A review of 2010 research in translational bioinformatics provides much to marvel at. We have seen notable advances in personal genomics, pharmacogenetics, and sequencing. At the same time, the infrastructure for the field has burgeoned. While acknowledging that, according to researchers, the members of this field tend to be overly optimistic, the authors predict a bright future.

Carcinoembryonic antigen-related cell adhesion molecule 16 interacts with alpha-tectorin and is mutated in autosomal dominant hearing loss (DFNA4).

We report on a secreted protein found in mammalian cochlear outer hair cells (OHC) that is a member of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family of adhesion proteins. Ceacam16 mRNA is expressed in OHC, and its protein product localizes to the tips of the tallest stereocilia and the tectorial membrane (TM). This specific localization suggests a role in maintaining the integrity of the TM as well as in the connection between the OHC stereocilia and TM, a linkage essential for mechanical amplification. In agreement with this role, CEACAM16 colocalizes and coimmunoprecipitates with the TM protein α-tectorin. In addition, we show that mutation of CEACAM16 leads to autosomal dominant nonsyndromic deafness (ADNSHL) at the autosomal dominant hearing loss (DFNA4) locus. In aggregate, these data identify CEACAM16 as an α-tectorin-interacting protein that concentrates at the point of attachment of the TM to the stereocilia and, when mutated, results in ADNSHL at the DFNA4 locus.