Using Environmental DNA to Detect Whales and Dolphins in the New York Bight

Determining how cetaceans and other threatened marine animals use coastal habitats is critical to the effective conservation of these species. Environmental DNA (eDNA) is an emerging tool that can potentially be used to detect cetaceans over broad spatial and temporal scales. In particular, eDNA may present a useful complementary method for monitoring their presence during visual surveys in nearshore areas, and for co-detecting prey. In conjunction with ongoing visual surveys, we tested the ability of eDNA metabarcoding to detect the presence and identity of cetaceans in the New York Bight (NYB), and to identify fish species (potential prey) present in the area. In almost all cases in which humpback whales and dolphins were visually observed, DNA from these species was also detected in water samples. To assess eDNA degradation over time, we took samples in the same location 15 and 30min after a sighting in seven instances, and found that eDNA often, but not always, dropped to low levels after 30min. Atlantic menhaden were detected in all samples and comprised the majority of fish sequences in most samples, in agreement with observations of large aggregations of this important prey species in the NYB. While additional data are needed to better understand how factors such as behavior and oceanographic conditions contribute to the longevity of eDNA signals, these results add to a growing body of work indicating that eDNA is a promising tool to complement visual and acoustic surveys of marine megafauna

Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins

Funding: E.C.G. was funded by a Royal Society Newton International Fellowship and Royal Society University Research Fellowship.In migratory marine species, investigating population connectivity and structure can be challenging given barriers to dispersal are less evident and multiple factors may influence individual movement patterns. Male humpback whales sing a song display that can provide insights into contemporary connectivity patterns, as there can be a cultural exchange of a single, population-wide shared song type with neighbouring populations in acoustic contact. Here, we investigated song exchange between populations located on the east and west coasts of Africa using 5 years of concurrent data (2001–2005). Songs were qualitatively and quantitatively transcribed by measuring acoustic features of all song units and then compared using both Dice’s similarity index and the Levenshtein distance similarity index (LSI) to quantitatively calculate song similarity. Song similarity varied among individuals and potentially between populations depending on the year (Dice: 36–100%, LSI: 21–100%), suggesting varying levels of population connectivity and/or interchange among years. The high degree of song sharing indicated in this study further supports genetic studies that demonstrate interchange between these two populations and reinforces the emerging picture of broad-scale connectivity in Southern Hemisphere populations. Further research incorporating additional populations and years would be invaluable for better understanding of fine-scale, song interchange patterns between Southern Hemisphere male humpback whales.Publisher PDFPeer reviewe

miR-125b Promotes Early Germ Layer Specification through Lin28/let-7d and Preferential Differentiation of Mesoderm in Human Embryonic Stem Cells

Unlike other essential organs, the heart does not undergo tissue repair following injury. Human embryonic stem cells (hESCs) grow indefinitely in culture while maintaining the ability to differentiate into many tissues of the body. As such, they provide a unique opportunity to explore the mechanisms that control human tissue development, as well as treat diseases characterized by tissue loss, including heart failure. MicroRNAs are small, non-coding RNAs that are known to play critical roles in the regulation of gene expression. We profiled the expression of microRNAs during hESC differentiation into myocardial precursors and cardiomyocytes (CMs), and determined clusters of human microRNAs that are specifically regulated during this process. We determined that miR-125b overexpression results in upregulation of the early cardiac transcription factors, GATA4 and Nkx2-5, and accelerated progression of hESC-derived myocardial precursors to an embryonic CM phenotype. We used an in silico approach to identify Lin28 as a target of miR-125b, and validated this interaction using miR-125b knockdown. Anti-miR-125b inhibitor experiments also showed that miR-125b controls the expression of miRNA let-7d, likely through the negative regulatory effects of Lin28 on let-7. We then determined that miR-125b overexpression inhibits the expression of Nanog and Oct4 and promotes the onset of Brachyury expression, suggesting that miR-125b controls the early events of human CM differentiation by inhibiting hESC pluripotency and promoting mesodermal differentiation. These studies identified miR-125b as an important regulator of hESC differentiation in general, and the development of hESC-derived mesoderm and cardiac muscle in particular. Manipulation of miR-125b-mediated pathways may provide a novel approach to directing the differentiation of hESC-derived CMs for cell therapy applications

Comparative functional analysis of aquaporins/glyceroporins in mammals and anurans

Maintenance of fluid homeostasis is critical to establishing and maintaining normal physiology. The landmark discovery of membrane water channels (aquaporins; AQPs) ushered in a new area in osmoregulatory biology that has drawn from and contributed to diverse branches of biology, from molecular biology and genomics to systems biology and evolution, and from microbial and plant biology to animal and translational physiology. As a result, the study of AQPs provides a unique and integrated backdrop for exploring the relationships between genes and genome systems, the regulation of gene expression, and the physiologic consequences of genetic variation. The wide species distribution of AQP family members and the evolutionary conservation of the family indicate that the control of membrane water flux is a critical biological process. AQP function and regulation is proving to be central to many of the pathways involved in individual physiologic systems in both mammals and anurans. In mammals, AQPs are essential to normal secretory and absorptive functions of the eye, lung, salivary gland, sweat glands, gastrointestinal tract, and kidney. In urinary, respiratory, and gastrointestinal systems, AQPs are required for proper urine concentration, fluid reabsorption, and glandular secretions. In anurans, AQPs are important in mediating physiologic responses to changes in the external environment, including those that occur during metamorphosis and adaptation from an aquatic to terrestrial environment and thermal acclimation in anticipation of freezing. Therefore, an understanding of AQP function and regulation is an important aspect of an integrated approach to basic biological research

NSAIDs Modulate CDKN2A, TP53, and DNA Content Risk for Progression to Esophageal Adenocarcinoma

BACKGROUND: Somatic genetic CDKN2A, TP53, and DNA content abnormalities are common in many human cancers and their precursors, including esophageal adenocarcinoma (EA) and Barrett's esophagus (BE), conditions for which aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) have been proposed as possible chemopreventive agents; however, little is known about the ability of a biomarker panel to predict progression to cancer nor how NSAID use may modulate progression. We aimed to evaluate somatic genetic abnormalities with NSAIDs as predictors of EA in a prospective cohort study of patients with BE. METHODS AND FINDINGS: Esophageal biopsies from 243 patients with BE were evaluated at baseline for TP53 and CDKN2A (p16) alterations, tetraploidy, and aneuploidy using sequencing; loss of heterozygosity (LOH); methylation-specific PCR; and flow cytometry. At 10 y, all abnormalities, except CDKN2A mutation and methylation, contributed to EA risk significantly by univariate analysis, ranging from 17p LOH (relative risk [RR] = 10.6; 95% confidence interval [CI] 5.2–21.3, p < 0.001) to 9p LOH (RR = 2.6; 95% CI 1.1–6.0, p = 0.03). A panel of abnormalities including 17p LOH, DNA content tetraploidy and aneuploidy, and 9p LOH was the best predictor of EA (RR = 38.7; 95% CI 10.8–138.5, p < 0.001). Patients with no baseline abnormality had a 12% 10-y cumulative EA incidence, whereas patients with 17p LOH, DNA content abnormalities, and 9p LOH had at least a 79.1% 10-y EA incidence. In patients with zero, one, two, or three baseline panel abnormalities, there was a significant trend toward EA risk reduction among NSAID users compared to nonusers (p = 0.01). The strongest protective effect was seen in participants with multiple genetic abnormalities, with NSAID nonusers having an observed 10-y EA risk of 79%, compared to 30% for NSAID users (p < 0.001). CONCLUSIONS: A combination of 17p LOH, 9p LOH, and DNA content abnormalities provided better EA risk prediction than any single TP53, CDKN2A, or DNA content lesion alone. NSAIDs are associated with reduced EA risk, especially in patients with multiple high-risk molecular abnormalities

Smaller total and subregional cerebellar volumes in posttraumatic stress disorder:a mega-analysis by the ENIGMA-PGC PTSD workgroup

Although the cerebellum contributes to higher-order cognitive and emotional functions relevant to posttraumatic stress disorder (PTSD), prior research on cerebellar volume in PTSD is scant, particularly when considering subregions that differentially map on to motor, cognitive, and affective functions. In a sample of 4215 adults (PTSD n = 1642; Control n = 2573) across 40 sites from the ENIGMA-PGC PTSD working group, we employed a new state-of-the-art deep-learning based approach for automatic cerebellar parcellation to obtain volumetric estimates for the total cerebellum and 28 subregions. Linear mixed effects models controlling for age, gender, intracranial volume, and site were used to compare cerebellum volumes in PTSD compared to healthy controls (88% trauma-exposed). PTSD was associated with significant grey and white matter reductions of the cerebellum. Compared to controls, people with PTSD demonstrated smaller total cerebellum volume, as well as reduced volume in subregions primarily within the posterior lobe (lobule VIIB, crus II), vermis (VI, VIII), flocculonodular lobe (lobule X), and corpus medullare (all p -FDR &lt; 0.05). Effects of PTSD on volume were consistent, and generally more robust, when examining symptom severity rather than diagnostic status. These findings implicate regionally specific cerebellar volumetric differences in the pathophysiology of PTSD. The cerebellum appears to play an important role in higher-order cognitive and emotional processes, far beyond its historical association with vestibulomotor function. Further examination of the cerebellum in trauma-related psychopathology will help to clarify how cerebellar structure and function may disrupt cognitive and affective processes at the center of translational models for PTSD.</p

Smaller total and subregional cerebellar volumes in posttraumatic stress disorder:a mega-analysis by the ENIGMA-PGC PTSD workgroup

Although the cerebellum contributes to higher-order cognitive and emotional functions relevant to posttraumatic stress disorder (PTSD), prior research on cerebellar volume in PTSD is scant, particularly when considering subregions that differentially map on to motor, cognitive, and affective functions. In a sample of 4215 adults (PTSD n = 1642; Control n = 2573) across 40 sites from the ENIGMA-PGC PTSD working group, we employed a new state-of-the-art deep-learning based approach for automatic cerebellar parcellation to obtain volumetric estimates for the total cerebellum and 28 subregions. Linear mixed effects models controlling for age, gender, intracranial volume, and site were used to compare cerebellum volumes in PTSD compared to healthy controls (88% trauma-exposed). PTSD was associated with significant grey and white matter reductions of the cerebellum. Compared to controls, people with PTSD demonstrated smaller total cerebellum volume, as well as reduced volume in subregions primarily within the posterior lobe (lobule VIIB, crus II), vermis (VI, VIII), flocculonodular lobe (lobule X), and corpus medullare (all p -FDR &lt; 0.05). Effects of PTSD on volume were consistent, and generally more robust, when examining symptom severity rather than diagnostic status. These findings implicate regionally specific cerebellar volumetric differences in the pathophysiology of PTSD. The cerebellum appears to play an important role in higher-order cognitive and emotional processes, far beyond its historical association with vestibulomotor function. Further examination of the cerebellum in trauma-related psychopathology will help to clarify how cerebellar structure and function may disrupt cognitive and affective processes at the center of translational models for PTSD.</p

Fin whale song characteristics and potential subpopulation identity in the New York Bight

Abstract Fin whale (Balaenoptera physalus) song can follow a highly consistent pattern, and regional differences in song patterns can be a valuable indicator of subpopulation identity and distribution. In the Northwest Atlantic, endangered fin whales are currently managed as a single stock despite previous identification of different regional song patterns, which indicates potential subpopulation structuring and vulnerability to anthropogenic disturbance if not managed accordingly. Here we document fin whale song in the New York Bight (NYB) from 2017 to 2020 using passive acoustic data to identify monthly and yearly trends in song patterns and to explore potential subpopulation structuring. The predominant song pattern observed was highly consistent with the pattern documented almost a decade prior in the NYB, with short inter-note intervals (INI) from fall–winter and long-INIs in the spring. However, in one song year the majority of songs were composed of long-INIs. This change in song pattern could be due to a shift in fin whale behavior or possibly multiple fin whale subpopulations using the NYB. Fin whales in the NYB may be particularly vulnerable to disturbance given the increasing anthropogenic pressures in this region, and further research into subpopulation structuring is needed to ensure adequate management of these endangered whales

Research Note: Evaluation of the incidence of white striping and underlying myopathic abnormalities affected by fast weight gain in commercially fed broiler chickens.

Significant improvements in genetics, nutrition, and food efficiency have had a great impact on the rapid growth of broilers, notably with increases in muscle mass. However, with rapid growth, the broiler industry has been negatively impacted by the increased incidence of myopathies, including white striping. White striping affects the pectoralis major muscle of broilers, particularly the larger breasts of rapidly growing modern commercial broiler lines. In this study, we documented the growth process of commercial broiler chickens from hatching to market weight at 6&nbsp;wk. Gross pathology and histopathology analyses were performed on pectoralis major muscle collected weekly from birds culled from 1 to 6&nbsp;wk. The severity of both gross and histologic pathologies in the breast muscle increased over time. White striping was initially observed at week 2, with a rise in the incidence and severity through the sixth week. Mild histopathology was noted in week 2, characterized by macrophage infiltration and limited phagocytosis of the muscle. Muscle condition deteriorated with age and weight gain, with more prevalent macrophages, phagocytosis, and interstitial fibroblasts. By week 5 and 6, there was severe myopathy including regions of obliterated muscle tissue. Linear regression models show a positive correlation between white striping, gross pathology, and histopathology relative to weight and age

Research Note: Evaluation of the incidence of white striping and underlying myopathic abnormalities affected by fast weight gain in commercially fed broiler chickens.

Significant improvements in genetics, nutrition, and food efficiency have had a great impact on the rapid growth of broilers, notably with increases in muscle mass. However, with rapid growth, the broiler industry has been negatively impacted by the increased incidence of myopathies, including white striping. White striping affects the pectoralis major muscle of broilers, particularly the larger breasts of rapidly growing modern commercial broiler lines. In this study, we documented the growth process of commercial broiler chickens from hatching to market weight at 6&nbsp;wk. Gross pathology and histopathology analyses were performed on pectoralis major muscle collected weekly from birds culled from 1 to 6&nbsp;wk. The severity of both gross and histologic pathologies in the breast muscle increased over time. White striping was initially observed at week 2, with a rise in the incidence and severity through the sixth week. Mild histopathology was noted in week 2, characterized by macrophage infiltration and limited phagocytosis of the muscle. Muscle condition deteriorated with age and weight gain, with more prevalent macrophages, phagocytosis, and interstitial fibroblasts. By week 5 and 6, there was severe myopathy including regions of obliterated muscle tissue. Linear regression models show a positive correlation between white striping, gross pathology, and histopathology relative to weight and age