Linking morphodynamic processes and Silvery Minnow habitat conditions in the Middle Rio Grande- Isleta Reach, New Mexico

2020 Fall.Includes bibliographical references.The Middle Rio Grande, located in central New Mexico, is home to the Rio Grande Silvery Minnow (RGSM), an endangered species of fish. Much of the RGSM's historical range has been lost due to natural and human-caused alterations to the river. For this study, the availability of RGSM habitat is analyzed in the Isleta reach, a segment of the Middle Rio Grande extending approximately 42 miles from Isleta Diversion dam to the confluence of Rio Puerco. To better understand spatial and temporal trends in morphology and channel geometry, the Isleta reach is delineated into six subreaches (I1, I2, I3, I4, I5, and I6). The purpose of this study is to identify connections between hydraulics, geomorphology, and biology to better explain the changing biological conditions in the river. To assess changes in geomorphology along the Isleta reach, the geomorphic conceptual model developed by Massong et al. (2010) was applied to representative cross-sections in each subreach. The model proposes two pathways that changes in the Middle Rio Grande can follow: aggrading (A) or migrating (M). Through inspection of aerial imagery and cross-sectional geometry data, it appears that the Isleta reach is in stage 3 and migrating stages, M4-M8, indicating high sediment transport capacity. River form was further classified using Cluer and Thorne's (2013) stream evolution model. In 2012, all subreaches were in stage 3 (i.e. degradation) of the model. One-dimensional modeling techniques were used to assess habitat availability for the RGSM from 1962 to 2012. Using the Hydrologic Engineering Center's River Analysis System (HEC-RAS), flow distribution slices were used to compute velocity and depth along a cross-section. Hydraulically suitable RGSM habitat for larvae, juvenile, and adult stages is determined using velocity and depth criteria for the fish proposed by Mortensen et al. (2019). The results suggest that habitat availability follows three typical patterns. Earlier years (1962 and 1972) showed "rounded" habitat curves, while later years (1992, 2002, and 2012) showed "step" and "hook" habitat curves. Detailed maps were produced in ArcMap that aid in the visualization of where RGSM habitat is located within the Isleta reach. These maps suggest that subreaches I1 to I3 contain the most habitat for all life stages. However, much of the habitat is disconnected and far away from the main channel, making it inaccessible to the fish. Through an analysis of restoration potential, it was determined that subreaches I2 to I4 may be areas of focus for river management to increase RGSM habitat. Time-integrated habitat metrics, originally developed by Doidge et al. (2020), is a method of interpolating cumulative RGSM habitat for each year between 1992 and 2019. This method requires input of annual habitat curves and daily discharge data. These inputs are used in a summation of simple linear equations that results in habitat metrics for each of the RGSM's life stages. The results show that larval and juvenile habitat metrics are more sensitive to changes in daily discharge than adult habitat metrics. Ecological relationships were inferred based on plots created by Mortensen et al. (2020) that relate habitat metrics, discharge, occurrence probability and lognormal density. Overall, larvae proved to be strong predictors of population dynamics

Death is Not the End: The Role of Reactive Oxygen Species in Driving Apoptosis-induced Proliferation

Apoptosis-induced proliferation (AiP) is a compensatory mechanism to maintain tissue size and morphology following unexpected cell loss during normal development, and may also be a contributing factor to cancer growth and drug resistance. In apoptotic cells, caspase-initiated signaling cascades lead to the downstream production of mitogenic factors and the proliferation of neighboring surviving cells. In epithelial Drosophila tissues, the Caspase-9 homolog Dronc drives AiP via activation of Jun N-terminal kinase (JNK); however, the specific mechanisms of JNK activation remain unknown. Using a model of sustained AiP that produces a hyperplastic phenotype in Drosophila eye and head tissue, I have found that caspase-induced activation of JNK during AiP depends on extracellular reactive oxygen species (ROS) generated by the NADPH oxidase Duox. I found these ROS are produced early in the death-regeneration process by undifferentiated epithelial cells that have initiated the apoptotic cascade. I also found that reduction of these ROS by mis-expression of extracellular catalases was sufficient to reduce the frequency of overgrowth associated with our model of AiP. I further observed that extracellular ROS attract and activate Drosophila macrophages (hemocytes), which may in turn trigger JNK activity in epithelial cells by signaling through the TNF receptor Grindelwald. We propose that signaling back and forth between epithelial cells and hemocytes by extracellular ROS and Grindelwald drives compensatory proliferation within the epithelium, and that in cases of persistent signaling, such as in our sustained model of AiP, hemocytes play a tumor promoting role, driving overgrowth

Killers creating new life: caspases drive apoptosis-induced proliferation in tissue repair and disease

Apoptosis is a carefully orchestrated and tightly controlled form of cell death, conserved across metazoans. As the executioners of apoptotic cell death, cysteine-dependent aspartate-directed proteases (caspases) are critical drivers of this cellular disassembly. Early studies of genetically programmed cell death demonstrated that the selective activation of caspases induces apoptosis and the precise elimination of excess cells, thereby sculpting structures and refining tissues. However, over the past decade there has been a fundamental shift in our understanding of the roles of caspases during cell death-a shift precipitated by the revelation that apoptotic cells actively engage with their surrounding environment throughout the death process, and caspases can trigger a myriad of signals, some of which drive concurrent cell proliferation regenerating damaged structures and building up lost tissues. This caspase-driven compensatory proliferation is referred to as apoptosis-induced proliferation (AiP). Diverse mechanisms of AiP have been found across species, ranging from planaria to mammals. In this review, we summarize the current knowledge of AiP and we highlight recent advances in the field including the involvement of reactive oxygen species and macrophage-like immune cells in one form of AiP, novel regulatory mechanisms affecting caspases during AiP, and emerging clinical data demonstrating the critical importance of AiP in cancer

Genetic models of apoptosis-induced proliferation decipher activation of JNK and identify a requirement of EGFR signaling for tissue regenerative responses in Drosophila

Recent work in several model organisms has revealed that apoptotic cells are able to stimulate neighboring surviving cells to undergo additional proliferation, a phenomenon termed apoptosis-induced proliferation. This process depends critically on apoptotic caspases such as Dronc, the Caspase-9 ortholog in Drosophila, and may have important implications for tumorigenesis. While it is known that Dronc can induce the activity of Jun N-terminal kinase (JNK) for apoptosis-induced proliferation, the mechanistic details of this activation are largely unknown. It is also controversial if JNK activity occurs in dying or in surviving cells. Signaling molecules of the Wnt and BMP families have been implicated in apoptosis-induced proliferation, but it is unclear if they are the only ones. To address these questions, we have developed an efficient assay for screening and identification of genes that regulate or mediate apoptosis-induced proliferation. We have identified a subset of genes acting upstream of JNK activity including Rho1. We also demonstrate that JNK activation occurs both in apoptotic cells as well as in neighboring surviving cells. In a genetic screen, we identified signaling by the EGFR pathway as important for apoptosis-induced proliferation acting downstream of JNK signaling. These data underscore the importance of genetic screening and promise an improved understanding of the mechanisms of apoptosis-induced proliferation

Seven features of safety in maternity units: a framework based on multisite ethnography and stakeholder consultation

Background: Reducing avoidable harm in maternity services is a priority globally. As well as learning from mistakes, it is important to produce rigorous descriptions of ‘what good looks like’. Objective: We aimed to characterise features of safety in maternity units and to generate a plain language framework that could be used to guide learning and improvement. Methods: We conducted a multisite ethnography involving 401 hours of non-participant observations 33 semistructured interviews with staff across six maternity units, and a stakeholder consultation involving 65 semistructured telephone interviews and one focus group. Results: We identified seven features of safety in maternity units and summarised them into a framework, named For Us (For Unit Safety). The features include: (1) commitment to safety and improvement at all levels, with everyone involved; (2) technical competence, supported by formal training and informal learning; (3) teamwork, cooperation and positive working relationships; (4) constant reinforcing of safe, ethical and respectful behaviours; (5) multiple problem-sensing systems, used as basis of action; (6) systems and processes designed for safety, and regularly reviewed and optimised; (7) effective coordination and ability to mobilise quickly. These features appear to have a synergistic character, such that each feature is necessary but not sufficient on its own: the features operate in concert through multiple forms of feedback and amplification. Conclusions: This large qualitative study has enabled the generation of a new plain language framework—For Us—that identifies the behaviours and practices that appear to be features of safe care in hospital-based maternity units

Detecting caspase activity in Drosophila larval imaginal discs

Caspases are a highly specialized class of cell death proteases. Since they are synthesized as inactive full-length zymogens, activation--at least of effector caspases and to some extent also of initiator caspases-requires a proteolytic cleavage event, generating a large and a small subunit, two of each forming the active caspase. The proteolytic cleavage event generates neo-epitopes at both the C-terminus of the large subunit and the N-terminus of the small subunit. The cleaved Caspase-3 (CC3) antibody was raised against the neo-epitope of the large subunit and thus detects only cleaved, but not full-length, Caspase-3. Although raised against human cleaved Caspase-3, the CC3 antibody cross-reacts in other species and detects cleaved caspases, most notably DrICE and Dcp-1, in Drosophila. This protocol describes the procedure for use of the CC3 antibody to detect caspase activity in larval imaginal discs in Drosophila

The Sound of Silence: Signaling by Apoptotic Cells

Apoptosis is a carefully choreographed process of cellular self-destruction in the absence of inflammation. During the death process, apoptotic cells actively communicate with their environment, signaling to both their immediate neighbors as well as distant sentinels. Some of these signals direct the anti-inflammatory immune response, instructing specific subsets of phagocytes to participate in the limited and careful clearance of dying cellular debris. These immunomodulatory signals can also regulate the activation state of the engulfing phagocytes. Other signals derived from apoptotic cells contribute to tissue growth control with the common goal of maintaining tissue integrity. Derangements in these growth control signals during prolonged apoptosis can lead to excessive cell loss or proliferation. Here, we highlight some of the most intriguing signals produced by apoptotic cells during the course of normal development as well as during physiological disturbances such as atherosclerosis and cancer

Sensor-based detection of a Haemonchus contortus (Barber's pole worm) infection in sheep

Haemonchus contortus, or Barber's Pole worm, is considered one of the most pathogenic parasites of sheep due to the production, profitability and animal welfare implications associated with infections. However, detection of H. contortus infections by routine observation of sheep flocks is difficult, and producers are usually unaware of a problem until animals are severely infected. The aim of the current study was to explore the potential for accelerometer-based activity monitoring to detect H. contortus infections in sheep. A three-month clinical study was conducted in Central Queensland, Australia, whereby 45, 12-month-old merino wethers were randomly allocated to one of three treatment groups: control (n = 9), low H. contortus infection (n = 18) or high H. contortus infection (n = 18). Infection occurred on Day 0, and accelerometer sensors were attached to a halter and deployed on all animals from Day 21 to Day 70. Animals were sampled weekly (faecal and blood) and treated with an anthelmintic on Day 56. Following the clinical period, five study animals were observed for a total of five hours to compare direct behavioral observations against accelerometer data. This was then used to develop a machine learning (ML) model to classify the accelerometer data into active or inactive behavior, which was further summarized to determine the proportion of time spent active per day. The most valuable features in the selected ML model were movement variation (MV), maximum X-axis value (MaxX), standard deviation of the X-axis (SDX), maximum Y-axis value (MaxY) and standard deviation of the Z-axis (SDZ). Linear mixed-effects models identified a significant difference in all sheep activity pre- and post-anthelmintic drench on Day 56 (P < 0.001). Conversely, there was no significant difference between activity levels of infected animals compared to controls (P = 0.14). To further explore how the activity of sheep changed with clinical presentations of H. contortus infections, weekly faecal egg count (FEC) and blood packed cell volume (PCV) were compared to sheep activity using a Spearman's rank correlation test. There was a weak but significant negative correlation between FEC and sheep activity (P < 0.001) and a weak but significant positive correlation between PCV and sheep activity (P < 0.001). In conclusion, this study has shown that accelerometer-based activity monitoring may be able to identify changes in sheep activity associated with clinical presentations of H. contortus infections and between periods prior to and following anthelmintic treatment. However, the ability to detect activity differences between infected and control animals was less clear. Further research is needed to determine the impact of individual behavior variability and flock dynamics when using on-animal sensors for the detection of behavioral changes associated with disease