Rhonda DeCook

Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis

The genetic control of gene expression during shoot development in Arabidopsis thaliana was analyzed by combining quantitative trait loci (QTL) and microarray analysis. Using oligonucleotide array data from 30 recombinant inbred lines derived from a cross of Columbia and Landsberg erecta ecotypes, the Arabidopsis genome was scanned for marker-by-gene linkages or so-called expression QTL (eQTL). Single-feature polymorphisms (SFPs) associated with sequence disparities between ecotypes were purged from the data. SFPs may alter the hybridization efficiency between cDNAs from one ecotype with probes of another ecotype. In genome scans, five eQTL hot spots were found with significant marker-by-gene linkages. Two of the hot spots coincided with classical QTL conditioning shoot regeneration, suggesting that some of the heritable gene expression changes observed in this study are related to differences in shoot regeneration efficiency between ecotypes. Some of the most significant eQTL, particularly those at the shoot regeneration QTL sites, tended to show cis-chromosomal linkages in that the target genes were located at or near markers to which their expression was linked. However, many linkages of lesser significance showed expected “trans-effects,” whereby a marker affects the expression of a target gene located elsewhere on the genome. Some of these eQTL were significantly linked to numerous genes throughout the genome, suggesting the occurrence of large groups of coregulated genes controlled by single markers.

Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078) have sequenced the Palomero Toluqueño (Palomero) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole). Gene expression variation in maize hybrids is influenced by distant DNA sequences subject to paternal genomic imprinting. Heterosis refers to the superior performance of hybrid progeny relative to their inbred parents, but the mechanisms responsible are unknown. Hybrids between the maize inbred lines B73 and Mo17 exhibit heterosis regardless of cross direction. These reciprocal hybrids differ from each other phenotypically, and 30 to 50% of their genes are differentially expressed. We identified ~4000 expression quantitative trait loci (eQTL) that allowed us to identify markers linked to variation in expression. We found that over three-quarters of these eQTL act in trans (78%) and that 86% of these differentially regulate transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. This result suggests that widespread imprinting contributes to the regulation of gene expression in maize hybrids.

Ear manipulations reveal a critical period for survival and dendritic development at the single-cell level in Mauthner neurons

Second‐order sensory neurons are dependent on afferents from the sense organs during a critical period in development for their survival and differentiation. Past research has mostly focused on whole populations of neurons, hampering progress in understanding the mechanisms underlying these critical phases. To move toward a better understanding of the molecular and cellular basis of afferent‐dependent neuronal development, we developed a new model to study the effects of ear removal on a single identifiable cell in the hindbrain of a frog, the Mauthner cell. Ear extirpation at various stages of Xenopus laevis development defines a critical period of progressively‐reduced dependency of Mauthner cell survival/differentiation on the ear afferents. Furthermore, ear removal results in a progressively decreased reduction in the number of dendritic branches. Conversely, addition of an ear results in an increase in the number of dendritic branches. These results suggest that the duration of innervation and the number of inner ear afferents play a quantitative role in Mauthner cell survival/differentiation, including dendritic development.

Mutational ataxia resulting from abnormal vestibular acquisition and processing is partially compensated for.

Due to the multisensory input into the balance system, the loss of one input, such as an ear, can generally be compensated for. However, when a mismatch or incomplete loss of inputs occurs, the ability to compensate for the stimulus misrepresentation may be compromised. The inner ear and cerebellum are important input and processing centers for balance but no genetic models have been generated to assess balance or compensation in the abnormal development of both these organs/brain areas. Important to their formation is regulation of proliferation mediated by the proto-oncogene N-Myc. Conditional knockouts (CKOs) of N-Myc using Tg(Pax2-Cre) have a misshapen and smaller ear with a fused utricle, saccule, and cochlea and absent horizontal canal, aberrant cochlear and vestibular innervations, and a size reduction in the cerebellum. CKOs are viable with obvious behavioral deficits, including circling behavior and unstable gait. To test the degree of ataxia and possible compensation of vestibular defects in these mutant mice, we use the Noldus Catwalk System to assess the gait of Tg(Pax2-Cre) N-Myc CKOs over five months. N-Myc CKOs perform worse than control littermates, in particular, in step regularity. We show that disrupting one member of the Myc family during embryonic development coincides with a differential loss of function in the cochlea compared to the vestibular apparatus. In addition, we show that the distortion in the ear morphology combined with a reduction of the cerebellum, rather than a complete loss of the vestibular-cerebellar pathway, leads to partial behavioral compensation that remains unchanged over time.

Review of gunshot injuries in cats and dogs and utility of a triage scoring system to predict short-term outcome: 37 cases (2003–2008)

OBJECTIVE To describe the signalment, wound characteristics, and treatment of gunshot injuries in cats and dogs in urban and rural environments, and to evaluate the utility of the animal trauma triage (ATT) score as an early predictor of survival to discharge from the hospital. DESIGN Retrospective case series. ANIMALS 29 dogs and 8 cats. PROCEDURES Medical records of cats and dogs evaluated for gunshot wounds from 2003 and 2008 at a private urban referral practice in Cedar Rapids, Iowa, and an urban veterinary teaching hospital in Ames, Iowa, were reviewed. Information collected included signalment, chief reason for evaluation, circumstance of the injury, general physical examination findings, wound characteristics, treatments provided, cost of care, survival to discharge from the hospital (yes vs no), and duration of hospital stay. For each animal, ATT scores were calculated and evaluated as a prognostic tool. RESULTS 37 animals met study inclusion criteria. Animals with higher ATT scores had a greater likelihood of poor outcome following gunshot injury. Animals with higher ATT scores, classified as low (< 4.5) or high (> 4.5), were found to have a longer duration of stay, classified as zero (0 days), short (1 to 3 days), or long (> 3 days). Young male dogs generally considered working breeds were overrepresented (29/37 [78.4%]). A preference for low-velocity, low-kinetic-energy firearms was identified (19/37 [52%]). The most numerous wounds were those inflicted to the limbs (12/37 [32.4%]), during low-visibility hours or hunting excursions. Calculated ATT scores on admission were higher in animals requiring blood products or surgical procedures and in nonsurvivors. CONCLUSIONS AND CLINICAL RELEVANCE Results of the present study suggested that regional preferences in breed ownership and firearm choice are responsible for variation in gunshot injury characteristics and management in animals sustaining injuries in rural and urban settings in Iowa. In cats and dogs, calculation of an ATT score may provide a useful predictor of the need for surgery or blood products, duration of stay, and likelihood of survival to discharge from the hospital.

N-Myc and L-Myc are essential for hair cell formation but not maintenance.

Sensorineural hearing loss results from damage to the hair cells of the organ of Corti and is irreversible in mammals. While hair cell regeneration may prove to be the ideal therapy after hearing loss, prevention of initial hair cell loss could provide even more benefit at a lower cost. Previous studies have shown that the deletion of Atoh1 results in embryonic loss of hair cells while the absence of Barhl1, Gfi1, and Pou4f3 leads to the progressive loss of hair cells in newborn mice. We recently reported that in the early embryonic absence of N-Myc (using Pax2-Cre), hair cells in the organ of Corti develop and remain until at least seven days after birth, with subsequent progressive loss. Thus, N-Myc plays a role in hair cell viability; however, it is unclear if this is due to its early expression in hair cell precursors and throughout the growing otocyst as it functions through proliferation or its late expression exclusively in differentiated hair cells. Furthermore, the related family member L-Myc is mostly co-expressed in the ear, including in differentiated hair cells, but its function has not been studied and could be partially redundant to N-Myc. To test for a long-term function of the Mycs in differentiated hair cells, we generated nine unique genotypes knocking out N-Myc and/or L-Myc after initial formation of hair cells using the well-characterized Atoh1-Cre. We tested functionality of the auditory and vestibular systems at both P21 and four months of age and under the administration of the ototoxic drug cisplatin. We conclude that neither N-Myc nor L-Myc is likely to play important roles in long-term hair cell maintenance. Therefore, it is likely that the late-onset loss of hair cells resulting from early deletion of the Mycs leads to an unsustainable developmental defect.

Canertinib–Induces Ototoxicity in Three Preclinical Models

Neuregulin-1 (NRG1) ligand and its epidermal growth factor receptor (EGFR)/ERBB family regulate normal cellular proliferation and differentiation in many tissues including the cochlea. Aberrant NRG1 and ERBB signaling cause significant hearing impairment in mice. Dysregulation of the same signaling pathway in humans is involved in certain types of cancers such as breast cancer or non-small cell lung cancer (NSCLC). A new irreversible pan-ERBB inhibitor, canertinib, has been tested in clinical trials for the treatment of refractory NSCLC. Its possible ototoxicity was unknown. In this study, a significant dose-dependent canertinib ototoxicity was observed in a zebrafish model. Canertinib ototoxicity was further confirmed in two mouse models with different genetic backgrounds. The data strongly suggested an evolutionally preserved ERBB molecular mechanism underlying canertinib ototoxicity. Thus, these results imply that clinical monitoring of hearing loss should be considered for clinical testing of canertinib or other pan-ERBB inhibitors.

Retrospective evaluation of plasma cholesterol concentration in septic dogs and its association with morbidity and mortality: 51 cases (2005-2015): Plasma cholesterol as a biomarker in sepsis

OBJECTIVE To determine whether plasma cholesterol concentrations in dogs with sepsis is associated with morbidity or in-hospital mortality. DESIGN Retrospective cohort study from 2005-2015. SETTING Two private referral centers. ANIMALS Fifty-one dogs diagnosed with sepsis. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Dogs were classified as septic if they displayed ≥2 criteria of the systemic inflammatory response syndrome in conjunction with a documented underlying infectious cause. Dogs were excluded if they had been diagnosed previously with any concurrent illness reported to alter plasma cholesterol concentrations. Plasma cholesterol concentrations at the time of sepsis diagnosis were statistically analyzed for association with morbidity, as measured by the presence of organ dysfunction, the number of dysfunctional organs, duration of hospitalization, cost of hospitalization, and in-hospital mortality. Twenty-eight (55%) dogs survived to discharge, 15 (29%) were euthanized during hospitalization, and 8 (16%) died despite treatment. While median cholesterol concentrations were significantly different when comparing survivors to discharge versus nonsurvivors who died naturally despite treatment (P = 0.0245), they were not significantly different when comparing survivors to all nonsurvivors (P = 0.1821). Receiver operating characteristic curve analysis showed a cholesterol cutoff of 4.5 mmol/L (174 mg/dL) with a sensitivity of 75% and a specificity of 50% for predicting in-hospital mortality. For surviving dogs, plasma cholesterol concentrations were not associated with increased length of hospital stay. Number of dysfunctional organs and plasma cholesterol concentration were the 2 most significant individual predictors for survival, and when incorporated into a multivariate logistic regression model used for prediction, the model yielded a sensitivity of 94% and specificity of 63%. CONCLUSION Plasma cholesterol concentration can provide prognostic information in dogs with sepsis. Further prospective studies investigating the role of cholesterol in sepsis are needed.