SHOX Whole Gene Duplications Are Overrepresented in SHOX Haploinsufficiency Phenotype Cohorts.

Transcription of SHOX is dependent upon the interaction of the gene with a complex array of flanking regulatory elements. Duplications that contain flanking regulatory elements but not the SHOX gene have been reported in individuals with SHOX haploinsufficiency syndromes, suggesting that alterations to the physical organisation or genomic architecture may affect SHOX transcription. Individuals with tall stature and an additional X or Y chromosome have an extra copy of both the SHOX gene and the entire SHOX regulatory region, so all three copies of SHOX can be expressed fully. However, for a duplication of the SHOX gene that does not include all of the flanking regulatory elements, the potential effect on SHOX expression is difficult to predict. We present nine unpublished individuals with a SHOX whole gene duplication in whom the duplication contains variable amounts of the SHOX regulatory region, and we review 29 similar cases from the literature where phenotypic data were clearly stated. While tall stature was present in a proportion of these cases, we present evidence that SHOX whole gene duplications can also result in a phenotype more typically associated with SHOX haploinsufficiency and are significantly overrepresented in Leri-Weill dyschondrosteosis and idiopathic short stature probands compared to population controls. Although similar-looking duplications do not always produce a consistent phenotype, there may be potential genotype-phenotype correlations regarding the duplication size, regulatory element content, and the breakpoint proximity to the SHOX gene. Although ClinGen does not currently consider SHOX whole gene duplications to be clinically significant, the ClinGen triplosensitivity score does not take into account the context of the duplication, and more is now known about SHOX duplications and the role of flanking elements in SHOX regulation. The evidence presented here suggests that these duplications should not be discounted without considering the extent of the duplication and the patient phenotype, and should be included in diagnostic laboratory reports as variants of uncertain significance. Given the uncertain pathogenicity of these duplications, any reports should encourage the exclusion of all other causes of short stature where possible.

Four decades of climatic fluctuations and fish recruitment stability across a marine-freshwater gradient.

Investigating the effects of climatic variability on biological diversity, productivity, and stability is key to understanding possible futures for ecosystems under accelerating climate change. A critical question for estuarine ecosystems is, how does climatic variability influence juvenile recruitment of different fish species and life histories that use estuaries as nurseries? Here we examined spatiotemporal abundance trends and environmental responses of 18 fish species that frequently spend the juvenile stage rearing in the San Francisco Estuary, CA, USA. First, we constructed multivariate autoregressive state-space models using age-0 fish abundance, freshwater flow (flow), and sea surface temperature data (SST) collected over four decades. Next, we calculated coefficients of variation (CV) to assess portfolio effects (1) within and among species, life histories (anadromous, marine opportunist, or estuarine dependent), and the whole community; and (2) within and among regions of the estuary. We found that species abundances varied over space and time (increasing, decreasing, or dynamically stable); and in 83% of cases, in response to environmental conditions (wet/dry, cool/warm periods). Anadromous species responded strongly to flow in the upper estuary, marine opportunist species responded to flow and/or SST in the lower estuary, and estuarine dependent species had diverse responses across the estuary. Overall, the whole community when considered across the entire estuary had the lowest CV, and life histories and species provided strong biological insurance to the portfolio (2.4- to 3.5-fold increases in stability, respectively). Spatial insurance also increased stability, although to a lesser extent (up to 1.6-fold increases). Our study advances the notion that fish recruitment stability in estuaries is controlled by biocomplexity-life history diversity and spatiotemporal variation in the environment. However, intensified drought and marine heatwaves may increase the risk of multiple consecutive recruitment failures by synchronizing species dynamics and trajectories via Moran effects, potentially diminishing estuarine nursery function.

Screening of a large Rubinstein-Taybi cohort identified many novel variants and emphasizes the importance of the CREBBP histone acetyltransferase domain.

Pathogenic variants within the CREBBP and EP300 genes account for the majority of individuals with Rubinstein-Taybi syndrome (RSTS). Data are presented from a large cohort of 395 individuals referred for diagnostic testing of CREBBP, and of the 19 CREBBP missense variants classified as likely pathogenic in this study, 17 were within the histone acetyltransferase (HAT) domain, providing evidence that this domain is critical to the normal function of the CREBBP protein (CBP). The data presented here, combined with other published results, suggest that the presence of a missense variant within the CBP HAT domain can be considered as moderate evidence of pathogenicity in the context of official variant interpretation guidelines. Within our study cohort, 129 had a pathogenic or likely pathogenic CREBBP variant and 5 had a variant of uncertain significance (VUS) which warranted familial studies. 147 of the remaining probands were also screened for EP300 and a further 16 pathogenic or likely pathogenic variants were identified, plus one VUS. Therefore, this analysis has provided a molecular diagnosis in at least 145 individuals with RSTS (37%) and identified a wide range of variants (n = 133) of which 103 were novel.

Calibrating temperature reconstructions from fish otolith oxygen isotope analysis for California's critically endangered Delta Smelt.

RATIONALE: Oxygen isotope ratios (δ18 O values) of fish otoliths (ear bones) are valuable geochemical tracers of water conditions and thermal life history. Delta Smelt (Hypomesus transpacificus) are osmerid forage fish endemic to the San Francisco Estuary, California, USA, that are on the verge of extinction. These fish exhibit a complex life history that allows them to survive in a dynamic estuarine environment; however, a rapidly warming climate threatens this thermally sensitive species. Here we quantify the accuracy and precision of using δ18 O values in otoliths to reconstruct the thermal life histories of Delta Smelt. METHODS: Delta Smelt were reared for 360 days using three different water sources with different ambient δ18 Owater values (-8.75‰, -5.28‰, and -4.06‰) and different water temperatures (16.4°C, 16.7°C, 18.7°C, and 20.5°C). Samples were collected after 170 days (n = 28) and 360 days (n = 14) post-hatch. In situ δ18 O values were measured from the core of the otolith to the dorsal edge using secondary ion mass spectrometry (SIMS) to reconstruct temporally resolved thermal life histories. RESULTS: The δ18 Ootolith values for Delta Smelt varied as a linear inverse function of water temperature: 1000 ln α = 18.39 (±0.43, 1SE)(103 TK-1 ) - 34.56 (±1.49, 1SE) and δ18 Ootolith(VPDB) - δ18 Owater (VPDB) = 31.34(±0.09, 1SE) - 0.19(±0.01, 1SE) × T ° C. When the ambient δ18 Owater value is known, this species-specific temperature-dependent oxygen isotope fractionation model facilitated the accurate (0.25°C) and precise (±0.37°C, 2σ) reconstruction of the water temperature experienced by the fish. In contrast, the use of existing general fractionation equations resulted in inaccurate temperature reconstructions. CONCLUSIONS: The species-specific δ18 Ootolith fractionation equation allowed for accurate and precise reconstructions of water temperatures experienced by Delta Smelt. Characterization of ambient δ18 Owater values remains a critical next step for reconstructing thermal life histories of wild Delta Smelt. This tool will provide new insights into habitat utilization, potential thermal refugia, and resilience to future warming for this critically endangered fish.

A proposed core curriculum for dental English education in Japan.

BACKGROUND: Globalization of the professions has become a necessity among schools and universities across the world. It has affected the medical and dental professions in terms of curriculum design and student and patient needs. In Japan, where medicine and dentistry are taught mainly in the Japanese language, profession-based courses in English, known as Medical English and Dental English, have been integrated into the existing curriculum among its 83 medical and 29 dental schools. Unfortunately, there is neither a core curriculum nor a model syllabus for these courses. METHODS: This report is based on a survey, two discussion forums, a workshop, and finally, the drafting of a proposed core curriculum for dental English approved by consensus of the participants from each university. RESULTS: The core curriculum covers the theoretical aspects, including dental English terms and oral pathologies; and practical aspects, including blended learning and dentist-patient communication. It is divided into modules and is recommended to be offered for at least two semesters. CONCLUSIONS: The core curriculum is expected to guide curriculum developers in schools where dental English courses are yet to be offered or are still in their early development. It may also serve as a model curriculum to medical and dental schools in countries in Asia, Europe, Africa, and Central and South America, where English is not the medium of instruction.

Effects of incubation temperature on the upper thermal tolerance of the imperiled longfin smelt (Spirinchus thaleichthys).

Upper thermal limits in many fish species are limited, in part, by the heart's ability to meet increased oxygen demand during high temperatures. Cardiac plasticity induced by developmental temperatures can therefore influence thermal tolerance. Here, we determined how incubation temperatures during the embryonic stage influence cardiac performance across temperatures during the sensitive larval stage of the imperiled longfin smelt. We transposed a cardiac assay for larger fish to newly hatched larvae that were incubated at 9°C, 12°C or 15°C. We measured heart rate over increases in temperature to identify the Arrhenius breakpoint temperature (TAB), a proxy for thermal optimum and two upper thermal limit metrics: temperature when heart rate is maximized (Tpeak) and when cardiac arrhythmia occurs (TArr). Higher incubation temperatures increased TAB, Tpeak and TArr, but high individual variation in all three metrics resulted in great overlap of individuals at TAB, Tpeak and TArr across temperatures. We found that the temperatures at which 10% of individuals reached Tpeak or TArr and temperatures at which number of individuals at TAB relative to Tpeak (ΔN(TAB,Tpeak)) was maximal, correlated more closely with upper thermal limits and thermal optima inferred from previous studies, compared to the mean values of the three cardiac metrics of the present study. Higher incubation temperatures increased the 10% Tpeak and TArr thresholds but maximum ΔN(TAB,Tpeak) largely remained the same, suggesting that incubation temperatures modulate upper thermal limits but not Topt for a group of larvae. Overall, by measuring cardiac performance across temperatures, we defined upper thermal limits (10% thresholds; Tpeak, 14.4-17.5°C; TArr, 16.9-20.2°C) and optima (ΔN(TAB,Tpeak), 12.4-14.4°C) that can guide conservation strategies for longfin smelt and demonstrated the potential of this cardiac assay for informing conservation plans for the early life stages of fish.

Triclosan and Methyl Triclosan in Prey Fish in a Wastewater-Influenced Estuary.

While the antimicrobial ingredient triclosan has been widely monitored in the environment, much less is known about the occurrence and toxicity of its major transformation product, methyl triclosan. An improved method was developed and validated to effectively extract and quantify both contaminants in fish tissue and used to characterize concentrations in small prey fish in areas of San Francisco Bay where exposure to triclosan via municipal wastewater discharges was expected to be highest. Concentrations of triclosan (0.44-57 ng/g wet wt, median 1.9 ng/g wet wt) and methyl triclosan (1.1-200 ng/g wet wt, median 36 ng/g wet wt) in fish tissue decreased linearly with concentrations of nitrate in site water, used as indicators of wastewater influence. The total concentrations of triclosan and methyl triclosan measured in prey fish were below available toxicity thresholds for triclosan, but there are few ecotoxicological studies to evaluate impacts of methyl triclosan. Methyl triclosan represented up to 96% of the total concentrations observed. These results emphasize the importance of monitoring contaminant transformation products, which can be present at higher levels than the parent compound. Environ Toxicol Chem 2023;42:620-627. © 2023 SETAC.

An analysis of publication trends of orthopedic surgery residency graduates in relation to academic achievement.

CONTEXT: Traditionally, the Accreditation Council for Graduate Medical Education (ACGME) requires residency programs to implement research and other scholarly activities into their training curriculum. Encouraging residents to publish during residency is believed to promote research throughout their careers; however, no study has attempted to quantify research productivity among orthopedic surgery residents before, during, and after residency. OBJECTIVES: To determine whether publishing in peer-reviewed journals during orthopedic residencies was an indicator of continued academic achievement after graduation. METHODS: This study was observational in nature and employed a cross-sectional design. We examined whether research outcomes during orthopedic residency was associated with academic advancement or continued research involvement after residency. We identified 201 orthopedic residency programs on the Doximity website and randomly selected 50 to include in our sample. Of these programs, graduate rosters for 31 programs were located and subsequently included. Of the 341 graduates identified, we recorded the number of peer-reviewed publications, H-indices, fellowships, and whether the graduate pursued a career in private practice or academia. RESULTS: Orthopedic residency graduates from 31 programs published a total of 1923 peer-reviewed manuscripts. On average, residents had a total of 5.6 publications and an h-index of 3.2. Residents entering academia and pursuing fellowships had a significantly higher total number of publications, higher number of first-author publications, and greater H-indices compared to those who did not enter academia or pursue a fellowship. CONCLUSIONS: Increased research productivity was associated with continued academic pursuits and an increased likelihood of pursuing fellowship training after residency.

Polygenic discrimination of migratory phenotypes in an estuarine forage fish.

Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined Restriction site Associated DNA sequencing data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, discriminant analysis of principal components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.

Growth, osmoregulation and ionoregulation of longfin smelt (Spirinchus thaleichthys) yolk-sac larvae at different salinities.

Longfin smelt (Spirinchus thaleichthys) is a threatened anadromous fish species that spawns in freshwater to moderately brackish (i.e. 5-10 ppt) reaches of the upper San Francisco Estuary and has declined to ~1% of its pre-1980s abundances. Despite 50+ years of population monitoring, the efficacy of 10+ years of conservation efforts for longfin smelt remain uncertain due to a limited understanding of how the species responds to environmental variation, such as salinity. For example, high mortality during larval stages has prevented culture efforts from closing the life cycle in captivity. Here, we investigated the effects of salinity on longfin smelt yolk-sac larvae. Newly hatched larvae from four single-pair crosses were acutely transferred to and reared at salinities of 0.4, 5, 10, 20 or 32 ppt. We compared whole-body water and sodium ion (Na+) content, notochord length and yolk-sac volume at 12, 24, 48, 72, and 96 hours post-transfer for each salinity treatment. We found that larvae maintained osmotic and ionic balance at 0.4-10 ppt, whereas salinities ˃10 ppt resulted in decreased water and increased whole-body Na+ content. We also found that larvae grew largest and survived the longest when reared at 5 and 10 ppt, respectively, and that yolk resorption stalled at 0.4 ppt. Finally, there were significant but small interclutch variations in responses to different salinities, with clutch accounting for <8% of the variance in our statistical models. Overall, our results indicate that longfin smelt yolk-sac larvae likely perform best at moderately brackish conditions, thus yielding a mechanism that explains their distribution in field surveys and providing key information for future conservation efforts.

Apparent Homozygosity for a gr/gr AZFc Deletion in A 47,XYY Man with Oligozoospermia and Secondary Infertility.

Background: Approximately 1 in 1000 men have a 47,XYY karyotype. Previous publications have presented cases of infertile XYY men and have suggested that the additional Y chromosome may cause disrupted meiosis leading to sperm apoptosis. The purpose of the current study was to determine whether XYY men are over-represented in infertility cohorts. Methods: In this paper, an ongoing infertility cohort was evaluated for Y chromosome microdeletions using the MLPA technique and the data from the first 2000 referrals were recorded. Moreover, the MLPA technique detected 47,XYY karyotypes. Results: Four XYY individuals were identified within the cohort. One of the four XYY men was shown to have an apparent gr/gr partial AZFc deletion on both Y chromosomes while Sertoli cell only syndrome was detected in another case. The other two cases (out of 2000) might, therefore, represent an incidental finding. Conclusion: The gr/gr deletion is not detectable by the multiplex PCR method; therefore, there might be additional explanations for the fertility problems of infertile XYY men reported in previously published articles. It seems that among other cases, their XYY karyotype may be coincidental, rather than causative of their fertility issues.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt.

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left-right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish.

BACKGROUND: The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species' vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. METHODS: Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. RESULTS: Overall, otolith size varied linearly with fish size (from 10-60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0-30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such experimental assessments across multiple developmental stages are key steps toward assessing confidence in otolith-derived metrics that are often used to assess the dynamics of wild fish populations.

Complex life histories discovered in a critically endangered fish.

Effective conservation of endangered species requires knowledge of the full range of life-history strategies used to maximize population resilience within a stochastic and ever-changing environment. California's endemic Delta Smelt (Hypomesus transpacificus) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as a semi-anadromous species, recent studies have challenged this lifecycle model for Delta Smelt, suggesting the species is an estuarine resident with several localized "hot-spots" of abundance. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life-history phenotypes including freshwater resident (FWR), brackish-water resident (BWR), and semi-anadromous (SA) fish. We further refined life-history phenotypes using an unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the semi-anadromous fish could be clustered into at least four additional life-history phenotypes that varied by natal origin, dispersal age and adult salinity history. These diverse life-history strategies should be incorporated into future conservation and management efforts aimed at preventing the extinction of Delta Smelt in the wild.

Role of freshwater floodplain-tidal slough complex in the persistence of the endangered delta smelt.

Seasonal floodplain wetland is one of the most variable and diverse habitats found in coastal ecosystems, yet it is also one of the most highly altered by humans. The Yolo Bypass, the primary floodplain of the Sacramento River in California's Central Valley, USA, has been shown to provide various benefits to native fishes when inundated. However, the Yolo Bypass exists as a tidal dead-end slough during dry periods and its value to native fishes has been less studied in this state. During the recent drought (2012-2016), we found higher abundance of the endangered Delta Smelt (Hypomesus transpacificus), than the previous 14 years of fish monitoring within the Yolo Bypass. Meanwhile, Delta Smelt abundance elsewhere in the estuary was at record lows during this time. To determine the value of the Yolo Bypass as a nursery habitat for Delta Smelt, we compared growth, hatch dates, and diets of juvenile Delta Smelt collected within the Yolo Bypass with fish collected among other putative nursery habitats in the San Francisco Estuary between 2010 and 2016. Our results indicated that when compared to other areas of the estuary, fish in the Yolo Bypass spawned earlier, and offspring experienced both higher quality feeding conditions and growth rates. The occurrence of healthy juvenile Delta Smelt in the Yolo Bypass suggested that the region may have acted as a refuge for the species during the drought years of 2012-2016. However, our results also demonstrated that no single region provided the best rearing habitat for juvenile Delta Smelt. It will likely require a mosaic of habitats that incorporates floodplain-tidal sloughs in order to promote the resilience of this declining estuarine fish species.

IsoFishR: An application for reproducible data reduction and analysis of strontium isotope ratios (87Sr/86Sr) obtained via laser-ablation MC-ICP-MS.

The IsoFishR application is a data reduction and analysis tool for laser-ablation strontium isotope data, following common best practices and providing reliable and reproducible results. Strontium isotope ratios (87Sr/86Sr) are a powerful geochemical tracer commonly applied in a wide range of scientific fields and laser-ablation inductively coupled mass spectrometry is considered the method of choice to obtain spatially resolved 87Sr/86Sr isotope ratios from a variety of sample materials. However, data reduction and analyses methods are variable between different research groups and research communities limiting reproducibility between studies. IsoFishR provides a platform to standardize these methods and can be used for both spot and time-resolved line transects. Furthermore, it provides advanced data analysis tools and filters for outlier removal, noise reduction, and visualization of time resolved data. The application can be downloaded from GitHub (https://github.com/MalteWillmes/IsoFishR) and the source code is available, encouraging future development and evolution of this software.

Liquid chromatographic determination of N-methyl carbamate pesticide residues at low parts-per-billion levels in eggs.

A reversed-phase liquid chromatographic (LC) method is presented for the analysis of N-methyl carbamate pesticide residues and piperonyl butoxide in eggs at levels as low as 2 microg/kg (ppb). The study was undertaken to provide data for dietary exposure estimates used in risk analysis. The method uses an acetonitrile extraction followed by liquid-liquid partitioning and normal-phase aminopropyl solid-phase extraction column cleanup. Determination of residues is by reversed-phase LC with an inline postcolumn reaction followed by fluorescence detection. The average recoveries of 21 fortified (most at 2.0 and 20.0 ppb) N-methyl carbamate pesticide residues and the carbamate metabolite 1-naphthol from eggs ranged from 70 to 107%. Recoveries of the pesticide synergist piperonyl butoxide ranged from 63 to 106%. Single-comb White Leghorn hens were treated with the carbamate carbaryl, and the eggs subsequently produced were analyzed for carbaryl and 1-naphthol residues.

Validation of otolith growth rate analysis using cadmium-exposed larval topsmelt (Atherinops affinis).

We applied otolith growth rate analysis to an investigation of cadmium (Cd)-exposed larval topsmelt (Atherinops affinis) to determine if growth rate was a more sensitive measure than somatic growth (body wt or length). Topsmelt otoliths, calcareous concretions in the fish inner ear, formed daily increments, and otolith growth was proportional to somatic growth. Nine-day posthatch larval topsmelt were exposed to Cd (0-100 ppb) in seawater for 14 d and fed low or high ration levels in separate experiments. Whereas Cd impaired topsmelt growth and growth rates, the extent of growth reduction was dependent on the ration level. At high ration levels, otolith and somatic growth rates of fish exposed to Cd (50 and 100 ppb) were significantly reduced; however, no differences in final mean weight and only marginal differences in final mean length of Cd-exposed topsmelt were observed. At low ration levels, we detected reductions in both somatic growth as well as otolith and somatic growth rates of topsmelt exposed to Cd (50 and 100 ppb). Otolith growth rate analysis was more sensitive than growth measurements of Cd-exposed topsmelt, because it allowed the detection of small differences in growth rates even when differences in somatic growth were not observed.

Contaminant and food limitation stress in an endangered estuarine fish.

The abundance of Delta Smelt (Hypomesus transpacificus), a fish species endemic to the upper San Francisco Estuary (SFE), is declining. Several causes for the population decline have been proposed, including food limitation and contaminant effects. Here, using juvenile Delta Smelt collected from throughout their range, we measured a suite of indices across three levels of biological organization (cellular, organ, individual) that reflect fish condition at temporal scales ranging from hours to weeks. Using these indices, the relative conditions of fish collected from five regions in the SFE were compared: Cache Slough, Sacramento River Deep Water Ship Channel, Confluence, Suisun Bay and Suisun Marsh. Fish sampled from Suisun Bay and, to a lesser extent the Confluence, exhibited relatively poor short-term nutritional and growth indices and morphometric condition, while fish from the freshwater regions of the estuary, and Cache Slough in particular, exhibited the most apparent histopathological signs of contaminant exposure. In contrast, fish from the Suisun Marsh region exhibited higher short-term nutrition and growth indices, and better morphometric and histopathological condition. For instance, fish collected from Suisun Marsh had a mean stomach fullness, expressed as a percentage of fish weight, that was 3.4-fold higher than fish collected from Suisun Bay, while also exhibiting an incidence of histopathological lesions that was 11-fold lower than fish collected from Cache Slough. Thus, our findings support the hypothesis that multiple stressors, including food limitation and contaminants, are contributing to the decline of Delta Smelt, and that these stressors influence Delta Smelt heterogeneously across space.