A Murine Model of Subarachnoid Hemorrhage

In this video publication a standardized mouse model of subarachnoid hemorrhage (SAH) is presented. Bleeding is induced by endovascular Circle of Willis perforation (CWp) and proven by intracranial pressure (ICP) monitoring. Thereby a homogenous blood distribution in subarachnoid spaces surrounding the arterial circulation and cerebellar fissures is achieved. Animal physiology is maintained by intubation, mechanical ventilation, and continuous on-line monitoring of various physiological and cardiovascular parameters: body temperature, systemic blood pressure, heart rate, and hemoglobin saturation. Thereby the cerebral perfusion pressure can be tightly monitored resulting in a less variable volume of extravasated blood. This allows a better standardization of endovascular filament perforation in mice and makes the whole model highly reproducible. Thus it is readily available for pharmacological and pathophysiological studies in wild type and genetically altered mice.     

Bioluminescence imaging: a shining future for cardiac regeneration

Advances in bioanalytical techniques have become crucial for both basic research and medical practice. One example, bioluminescence imaging (BLI), is based on the application of natural reactants with light‐emitting capabilities (photoproteins and luciferases) isolated from a widespread group of organisms. The main challenges in cardiac regeneration remain unresolved, but a vast number of studies have harnessed BLI with the discovery of aequorin and green fluorescent proteins. First described in the luminous hydromedusan Aequorea victoria in the early 1960s, bioluminescent proteins have greatly contributed to the design and initiation of ongoing cell‐based clinical trials on cardiovascular diseases. In conjunction with advances in reporter gene technology, BLI provides valuable information about the location and functional status of regenerative cells implanted into numerous animal models of disease. The purpose of this review was to present the great potential of BLI, among other existing imaging modalities, to refine effectiveness and underlying mechanisms of cardiac cell therapy. We recount the first discovery of natural primary compounds with light‐emitting capabilities, and follow their applications to bioanalysis. We also illustrate insights and perspectives on BLI to illuminate current efforts in cardiac regeneration, where the future is bright.     

Preparing to Work with Big Data in Proteomics – A Report on the HUPO‐PSI Spring Workshop

The Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. The 2013 annual spring workshop was hosted by the University of Liverpool, UK and concentrated on updating and refining the existing standards in the light of new methodologies and technologies. To control the inflation of file sizes, strategies for file compression, particularly for mzML files, were explored. Best practices for encoding information such as protein grouping and PTM localisation were refined and documented. Additional example files for the mzQuantML format were designed to provide support for selected reaction monitoring techniques. Enhancements to the PSI Common Query Interface (PSICQUIC) and PSI‐MI XML were discussed. Finally, the group engaged in discussion on how the existing work of the HUPO‐PSI can be leveraged by the Metabolomics Standards Initiative to improve the capture of metabolite data.     

Use of environmental DNA to detect Eastern Sand Darter (Ammocrypta pellucida Putnam, 1863) in large Laurentian Great Lakes embayments

A single-species environmental DNA (eDNA) method was developed to sample for a small, benthic rare species, Eastern Sand Darter (Ammocrypta pellucida Putnam, 1863) in two large Lake Ontario embayments. Summer water sampling allowed for: (a) surveys of habitats (Wellers Bay) where traditional fish sampling gear could not be used; and, (b) a comparison between eDNA and seining-based detection probabilities at known occupied habitats (West Lake). In 2018, replicate (n = 3) 1 L water samples were collected from 90 Wellers Bay sites and 71 West Lake sites. A site-occupancy model, a hierarchical logistic regression model, was fitted to determine site occupancy, sample occupancy (presence of Eastern Sand Darter DNA in a water sample) and probability of detection (p) based on replicate quantitative polymerase chain reaction (qPCR) results for each water sample. Eastern Sand Darter was detected at 10 West Lake sites, but not from Wellers Bay. Mean site occupancy was 0.31 (0.12–0.70; 95% CLs), mean sample occupancy was 0.28 (0.09–0.58; 95% CLs), and mean detection probability in a subsample (i.e., successful qPCR amplification) given it was present was 0.40 (0.25–0.55; 95% CLs). While the eDNA method successfully detected Eastern Sand Darter from known occupied areas in West Lake, it was not more effective for assessing local site occupancy than traditional sampling methods, such as the seine.     

Dogs Detect Larger Wind Energy Effects on Bats and Birds

As wind turbine-caused mortality of birds and bats increases with increasing wind energy capacity, accurate fatality estimates are needed to assess effects, identify collision factors, and formulate mitigation. Finding a larger proportion of collision victims reduces the magnitude of adjustment for the proportion not found, thus reducing opportunities for bias. We tested detection dogs in trials of bat and small-bird carcasses placed randomly in routine fatality monitoring at the Buena Vista and Golden Hills Wind Energy projects, California, USA, 2017. Of trial carcasses placed and confirmed available before next-day fatality searches, dogs detected 96% of bats and 90% of small birds, whereas humans at a neighboring wind project detected 6% of bats and 30% of small birds. At Golden Hills dogs found 71 bat fatalities in 55 searches compared to 1 bat found by humans in 69 searches within the same search plots over the same season. Dog detection rates of trial carcasses remained unchanged with distance from turbine, and dogs found more fatalities than did humans at greater distances from turbines. Patterns of fatalities found by dogs within search plots indicated 20% of birds and 4–14% of bats remained undetected outside search plots at Buena Vista and Golden Hills. Dogs also increased estimates of carcass persistence by finding detection trial carcasses that the trial administrator had erroneously concluded were removed. Compared to human searches, dog searches resulted in fatality estimates up to 6.4 and 2.7 times higher for bats and small birds, respectively, along with higher relative precision and >90% lower cost per fatality detection. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

A practical guide to DNA metabarcoding for entomological ecologists

1. DNA metabarcoding is a cost-effective species identification approach with great potential to assist entomological ecologists. This review presents a practical guide to help entomological ecologists design their own DNA metabarcoding studies and ensure that sound ecological conclusions can be obtained. 2. The review considers approaches to field sampling, laboratory work, and bioinformatic analyses, with the aim of providing the background knowledge needed to make decisions at each step of a DNA metabarcoding workflow. 3. Although most conventional sampling methods can be adapted to DNA metabarcoding, this review highlights techniques that will ensure suitable DNA preservation during field sampling and laboratory storage. The review also calls for a greater understanding of the occurrence, transportation, and deposition of environmental DNA when applying DNA metabarcoding approaches for different ecosystems. 4. Accurate species detection with DNA metabarcoding needs to consider biases introduced during DNA extraction and PCR amplification, cross-contamination resulting from inappropriate amplicon library preparation, and downstream bioinformatic analyses. Quantifying species abundance with DNA metabarcoding is in its infancy, yet recent studies demonstrate promise for estimating relative species abundance from DNA sequencing reads. 5. Given that bioinformatics is one of the biggest hurdles for researchers new to DNA metabarcoding, several useful graphical user interface programs are recommended for sequence data processing, and the application of emerging sequencing technologies is discussed.     

A citizen science approach to long-term monitoring of humpback whales (Megaptera novaeangliae) off Sydney,Australia

The Cape Solander Whale Migration Study is a citizen science project that annually counts northward migrating humpback whales (Megaptera novaeangliae) off Cape Solander, Sydney, Australia. Dedicated observers have compiled a 20-year data set (1997–2017) of shore-based observations from Cape Solander's high vantage point. Using this long-term data set collected by citizen scientists, we sought to estimate the humpback whale population trend as it continues to recover postexploitation. We estimated an exponential growth rate of 0.099 (95% CI = 0.079–0.119) using a generalized linear model, based on observer effort (number of observation days) and number of whales observed, equating to 10% per annum growth in sightings since 1997. We found that favorable weather conditions for spotting whales off Cape Solander consisted of winds <30 km/hr from a southerly through a north westerly direction. Incidental observations of other cetacean species included the endangered blue whale (Balaenoptera musculus) and data deficient species such as killer whales (Orcinus orca) and false killer whales (Pseudorca crassidens). Citizen science-based studies can provide a cost-effective approach to monitoring wildlife over the time necessary to detect change in a population. Information obtained from citizen science projects like this may help inform policy makers responsible for State and Federal protection of cetaceans in Australian waters and beyond.     

Real-time dissolved carbon dioxide monitoring I: Application of a novel in situ sensor for CO2 monitoring and control

Dissolved carbon dioxide (dCO₂) is a well-known critical parameter in bioprocesses due to its significant impact on cell metabolism and on product quality attributes. Processes run at small-scale faces many challenges due to limited options for modular sensors for online monitoring and control. Traditional sensors are bulky, costly, and invasive in nature and do not fit in small-scale systems. In this study, we present the implementation of a novel, rate-based technique for real-time monitoring of dCO₂ in bioprocesses. A silicone sampling probe that allows the diffusion of CO₂ through its wall was inserted inside a shake flask/bioreactor and then flushed with air to remove the CO₂ that had diffused into the probe from the culture broth (sensor was calibrated using air as zero-point calibration). The gas inside the probe was then allowed to recirculate through gas-impermeable tubing to a CO₂ monitor. We have shown that by measuring the initial diffusion rate of CO₂ into the sampling probe we were able to determine the partial pressure of the dCO₂ in the culture. This technique can be readily automated, and measurements can be made in minutes. Demonstration experiments conducted with baker's yeast and Yarrowia lipolytica yeast cells in both shake flasks and mini bioreactors showed that it can monitor dCO₂ in real-time. Using the proposed sensor, we successfully implemented a dCO₂-based control scheme, which resulted in significant improvement in process performance.     

Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus

The Sage Grouse Centrocercus urophasianus is a species of conservation concern throughout its range in western North America. Since the 1950s, the high count of males at leks has been used as an index for monitoring populations. However, the relationship between this lek-count index and population size is unclear, and its reliability for assessing population trends has been questioned. We used non-invasive genetic mark-recapture analysis of faecal and feather samples to estimate pre-breeding population size for the Parachute-Piceance-Roan, a small, geographically isolated population of Sage Grouse in western Colorado, during two consecutive winters from 2012 to 2014. We estimated total pre-breeding population size as 335 (95% confidence interval (CI): 287–382) in the first winter and 745 (95% CI: 627–864) in the second, an approximate doubling in abundance between years. Although we also observed a large increase in the spring lek-count index between those years, high male count data poorly represented mark-recapture estimates of male abundance in each year. Our data suggest that lek counts are useful for detecting the direction and magnitude of large changes in Sage Grouse abundance over time but they may not reliably reflect small changes in abundance that may be relevant to small populations of conservation concern.     

The decline and rise of the Kransberg Cape Vulture colony over 35 years has implications for composite population indices and survey frequency

Long-term monitoring is key for detecting population declines. Composite indices allow researchers to combine trends from disparate monitoring programmes into a single estimate of population change. Inferences from composite indices, however, are limited to the time periods and areas studied. We show that the number of breeding pairs in a colony of Cape Vultures Gyps coprotheres in South Africa declined between the years 1983 and 2003 but increased in both the number of breeding pairs and fledglings per pair from 2004 to 2017. We performed a retrospective power analysis determining the minimum annual frequency with which the colony could have been monitored without sacrificing inference into population trends. This power analysis revealed the post-2003 population increase would not have been apparent if we skipped more than 2 years between surveys. We incorporated our estimates into a previously published composite index for Cape Vultures that considered only data collected pre-2000 and demonstrate that the inference is unchanged if the trend from the decline period or the entire study is incorporated, yet if only the trend during the period of population increase is used, there is no longer a statistically significant decline across the species’ range. Our results demonstrate the utility of long-term monitoring because if our study had concluded before 2003, there would be little evidence of the current population increase at Kransberg.