Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression.

Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.

Increased dominance of heat-tolerant symbionts creates resilient coral reefs in near-term ocean warming.

Climate change is radically altering coral reef ecosystems, mainly through increasingly frequent and severe bleaching events. Yet, some reefs have exhibited higher thermal tolerance after bleaching severely the first time. To understand changes in thermal tolerance in the eastern tropical Pacific (ETP), we compiled four decades of temperature, coral cover, coral bleaching, and mortality data, including three mass bleaching events during the 1982 to 1983, 1997 to 1998 and 2015 to 2016 El Niño heatwaves. Higher heat resistance in later bleaching events was detected in the dominant framework-building genus, Pocillopora, while other coral taxa exhibited similar susceptibility across events. Genetic analyses of Pocillopora spp. colonies and their algal symbionts (2014 to 2016) revealed that one of two Pocillopora lineages present in the region (Pocillopora "type 1") increased its association with thermotolerant algal symbionts (Durusdinium glynnii) during the 2015 to 2016 heat stress event. This lineage experienced lower bleaching and mortality compared with Pocillopora "type 3", which did not acquire D. glynnii. Under projected thermal stress, ETP reefs may be able to preserve high coral cover through the 2060s or later, mainly composed of Pocillopora colonies that associate with D. glynnii. However, although the low-diversity, high-cover reefs of the ETP could illustrate a potential functional state for some future reefs, this state may only be temporary unless global greenhouse gas emissions and resultant global warming are curtailed.

FAVOR: functional annotation of variants online resource and annotator for variation across the human genome.

Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https://favor.genohub.org.

Heat stress increases immune cell function in Hexacorallia.

Climate change induced heat stress has increased coral bleaching events worldwide. Differentially regulated immune genes are one of the primary responses to heat stress suggesting that immune activation is critical. However, the cellular immune mechanisms of coral bleaching is currently unknown, and it is still not known if the immune response documented during heat stress is a consequence of bleaching or is directly caused by the heat stress itself. To address this question, we have used two model system sea anemones (Order: Actiniaria): Exaiptasia diaphana and Nematostella vectensis. E. diaphana is an established sea anemone model for algal symbiont interaction, while N. vectensis is an established sea anemone model that lacks the algal symbiont. Here, we examined the effect of increased temperature on phagocytic activity, as an indication of immune function. Our data shows that immune cell activity increases during heat stress, while small molecule pinocytosis remains unaffected. We observed an increase in cellular production of reactive oxygen species with increasing temperatures. We also found that the cellular immune activity was not affected by the presence of the Symbiodiniaceae. Our results suggest that the immune activity observed in heat-stress induced bleaching in corals is a fundamental and basic response independent of the bleaching effect. These results establish a foundation for improving our understanding of hexacorallian immune cell biology, and its potential role in coral bleaching.

Functional Characterization of Hexacorallia Phagocytic Cells.

Phagocytosis is the cellular defense mechanism used to eliminate antigens derived from dysregulated or damaged cells, and microbial pathogens. Phagocytosis is therefore a pillar of innate immunity, whereby foreign particles are engulfed and degraded in lysolitic vesicles. In hexacorallians, phagocytic mechanisms are poorly understood, though putative anthozoan phagocytic cells (amoebocytes) have been identified histologically. We identify and characterize phagocytes from the coral Pocillopora damicornis and the sea anemone Nematostella vectensis. Using fluorescence-activated cell sorting and microscopy, we show that distinct populations of phagocytic cells engulf bacteria, fungal antigens, and beads. In addition to pathogenic antigens, we show that phagocytic cells engulf self, damaged cells. We show that target antigens localize to low pH phagolysosomes, and that degradation is occurring within them. Inhibiting actin filament rearrangement interferes with efficient particle phagocytosis but does not affect small molecule pinocytosis. We also demonstrate that cellular markers for lysolitic vesicles and reactive oxygen species (ROS) correlate with hexacorallian phagocytes. These results establish a foundation for improving our understanding of hexacorallian immune cell biology.

"What do you think about nephrology?" A national survey of internal medicine residents.

BACKGROUND: Interest in nephrology has been declining among internal medicine residents but the reasons behind this observation are not well characterized. Our objective was to evaluate factors influencing residents' choice of subspecialty. METHODS: This is a mixed-method QUAL-QUAN design study that used the results of our previously published qualitative analysis on residents' perception of nephrology to create and pilot a questionnaire of 60 questions. The final questionnaire was distributed to 26 programs across the United States and a total of 1992 residents. We calculated response rates and tabulated participant characteristics and percentage of participant responses. We categorized choice of fellowship into 2 medical categories (Highly Sought After vs. Less Sought After) and fitted a logistic regression model of choosing a highly vs. less sought after fellowship. RESULTS: Four hundred fifteen out of 1992 (21%) US residents responded to the survey. Of the 268 residents planning to pursue fellowship training, 67 (25%) selected a less sought after fellowship. Female sex was associated with significantly higher odds of selecting a less sought after fellowship (OR = 2.64, 95% CI: 1.47, 4.74). Major factors deterring residents from pursuing nephrology were perception of inadequate financial compensation, broad scope of clinical practice and complexity of patient population. We observed a decline in exposure to nephrology during the clinical years of medical school with only 35.4% of respondents rotating in nephrology versus 76.8% in residency. The quality of nephrology education was rated less positively during clinical medical school years (median of 50 on a 0-100 point scale) compared to the pre-clinical years (median 60) and residency (median 75). CONCLUSION: Our study attempts to explain the declining interest in nephrology. Results suggest potential targets for improvement: diversified trainee exposure, sub-specialization of nephrology, and increased involvement of nephrologists in the education of trainees.

Fluorescence-Activated Cell Sorting for the Isolation of Scleractinian Cell Populations.

Coral reefs are under threat due to anthropogenic stressors. The biological response of coral to these stressors may occur at a cellular level, but the mechanisms are not well understood. To investigate coral response to stressors, we need tools for analyzing cellular responses. In particular, we need tools that facilitate the application of functional assays to better understand how cell populations are reacting to stress. In the current study, we use fluorescence-activated cell sorting (FACS) to isolate and separate different cell populations in stony corals. This protocol includes: (1) the separation of coral tissues from the skeleton, (2) creation of a single cell suspension, (3) labeling the coral cells using various markers for flow cytometry, and (4) gating and cell sorting strategies. This method will enable researchers to work on corals at the cellular level for analysis, functional assays, and gene expression studies of different cell populations.

Performance of Creatinine Clearance and Estimated GFR in Assessing Kidney Function in Living Donor Candidates.

BACKGROUND: Glomerular filtration rate (GFR) assessment is a key aspect in the evaluation of living kidney donor candidates; however, data on performance of commonly used methods are limited. METHODS: We examined 769 living kidney donor candidates with 24-hour urine collections assessed as accurate by comparing measured creatinine excretion rate (CER) to CER estimated using a 4-variable equation previously developed and validated using robust methodology. RESULTS: Of all collections, 42.6% would have been deemed inaccurate, mostly under-collections, using the conventional weight- and gender-based CER estimation. Creatinine clearance (CrCl) overestimated I-iothalamate GFR (iGFR), estimated GFR (eGFR), underestimated iGFR, and their average [Avg (CrCl and eGFR)] essentially eliminated the GFR bias (median bias = +2.2, -5.4, and -1.0 mL/min/1.73 m, respectively; P < 0.001). This held true for all subgroups except blacks, where all 3 measures overestimated iGFR. Avg (CrCl and eGFR) also offered modestly improved accuracy compared with CrCl alone, as measured by the proportion of values falling within 10% (50.7% versus 45.3%; P = 0.009) and 30% of iGFR (94.5% versus 89.3%; P < 0.001). CONCLUSIONS: When measured GFR is unavailable, the Avg (CrCl and eGFR) provides a better estimate of kidney function in kidney donor candidates than either measure alone, although in blacks the estimates are neither better nor worse.

Hypogonadism and testosterone replacement therapy in end-stage renal disease (ESRD) and transplant patients.

Hypogonadism is a common problem in the end-stage renal disease (ESRD) and renal transplant population. It has widespread systemic effects and has been linked with mortality in dialysis patients and at the time of renal transplant. The etiology is likely multifactorial and most patients are afflicted by various comorbidities that can contribute to hypogonadism. Clinical manifestations are mostly nonspecific. We review the approach to the diagnosis of hypogonadism, focusing on both laboratory values and clinical signs and symptoms. We review treatment with testosterone replacement in this population and highlight various studies that tend to have small sample sizes. Though these studies provide insight into testosterone replacement, the need for larger studies is emphasized to better understand the effects and safety of therapy.

Stone characteristics on noncontrast computed tomography: establishing definitive patterns to discriminate calcium and uric acid compositions.

OBJECTIVE: To evaluate if different stone compositions can be distinguished by variations in Hounsfield unit (HU) patterns from stone core to periphery. MATERIALS AND METHODS: We retrospectively reviewed our stone registry searching for pure uric acid (UA) and calcium oxalate (CaOx) stones. Inclusion criteria comprised: pure calculi; noncontrast computed tomography before stone analysis; and stone size ≥4 mm. A single urologist reviewed all images (abdominal/bone windows). Absolute HU attenuation was measured in the center (core) and edges (periphery) of each stone. HU density (HU/size) and stone volume were calculated. Categorical variables were compared with Chi-square/Fisher exact test; continuous with analysis of variance/Student t test. Spearman's test was used correlate HU values and stone dimensions. A P <.05 was considered significant. RESULTS: Included were 47 UA and 36 CaOx stones. CaOx cohort had higher HU values for all parameters (P <.001). HU variation (core-periphery) was more homogeneous in the UA group (-25%) than in the CaOx group (-52%). Stone dimensions had a significant positive correlation with HU values in CaOx cohort. In the UA group, stone volume and periphery HU had significant positive correlation. On bone window, CaOx stones had a heterogeneous pattern with a higher attenuation core with decreasing attenuation toward the periphery; UA calculi had a more homogeneous constant frosted white cloudy appearance. CONCLUSION: Stone size does not affect HU for UA stone, but has a positive correlation with CaOx stone. UA stones can be differentiated from CaOx by evaluating variation in HU from core to periphery and by subjective evaluation of homogeneity in bone windows.

Absolute Hounsfield unit measurement on noncontrast computed tomography cannot accurately predict struvite stone composition.

BACKGROUND: The purpose of our study was to determine, in vivo, whether single-energy noncontrast computed tomography (NCCT) can accurately predict the presence/percentage of struvite stone composition. METHODS: We retrospectively searched for all patients with struvite components on stone composition analysis between January 2008 and March 2012. Inclusion criteria were NCCT prior to stone analysis and stone size ≥4 mm. A single urologist, blinded to stone composition, reviewed all NCCT to acquire stone location, dimensions, and Hounsfield unit (HU). HU density (HUD) was calculated by dividing mean HU by the stone's largest transverse diameter. Stone analysis was performed via Fourier transform infrared spectrometry. Independent sample Student's t-test and analysis of variance (ANOVA) were used to compare HU/HUD among groups. Spearman's correlation test was used to determine the correlation between HU and stone size and also HU/HUD to % of each component within the stone. Significance was considered if p<0.05. RESULTS: Fourty-four patients met the inclusion criteria. Struvite was the most prevalent component with mean percentage of 50.1%±17.7%. Mean HU and HUD were 820.2±357.9 and 67.5±54.9, respectively. Struvite component analysis revealed a nonsignificant positive correlation with HU (R=0.017; p=0.912) and negative with HUD (R=-0.20; p=0.898). Overall, 3 (6.8%) had <20% of struvite component; 11 (25%), 25 (56.8%), and 5 (11.4%) had 21% to 40%, 41% to 60%, and 61% to 80% of struvite, respectively. ANOVA revealed no difference among groups regarding HU (p=0.68) and HUD (p=0.37), with important overlaps. When comparing pure struvite stones (n=5) with other miscellaneous stones (n=39), no difference was found for HU (p=0.09) but HUD was significantly lower for pure stones (27.9±23.6 v 72.5±55.9, respectively; p=0.006). Again, significant overlaps were seen. CONCLUSIONS: Pure struvite stones have significantly lower HUD than mixed struvite stones, but overlap exists. A low HUD may increase the suspicion for a pure struvite calculus.