Persistence of DNA in Carcasses, Slime and Avian Feces May Affect Interpretation of Environmental DNA Data

<div><p>The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp; <i>Hypophthalmichthys molitrix</i> and <i>H. nobilis</i>) in the Chicago Area Waterway System and Upper Mississippi River. In both systems DNA has been detected from silver carp without the capture of a live fish, which has led to some uncertainty about the source of the DNA. The potential contribution to eDNA by vectors and fomites has not been explored. Because barges move from areas with a high abundance of bigheaded carps to areas monitored for the potential presence of silver carp, we used juvenile silver carp to simulate the barge transport of dead bigheaded carp carcasses, slime residue, and predator feces to determine the potential of these sources to supply DNA to uninhabited waters where it could be detected and misinterpreted as indicative of the presence of live bigheaded carp. Our results indicate that all three vectors are feasible sources of detectable eDNA for at least one month after their deposition. This suggests that current monitoring programs must consider alternative vectors of DNA in the environment and consider alternative strategies to minimize the detection of DNA not directly released from live bigheaded carps.</p></div

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor.

Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for all computationally intense problems. High-throughput computing (HTC) is one method for handling computationally intense research. In contrast to high-performance computing, which uses a single "supercomputer," HTC can distribute tasks over many computers (e.g., idle desktop computers, dedicated servers, or cloud-based resources). HTC facilities exist at many academic and government institutes and are relatively easy to create from commodity hardware. Additionally, consortia such as Open Science Grid facilitate HTC, and commercial entities sell cloud-based solutions for researchers who lack HTC at their institution. We provide an introduction to HTC for biologists and environmental scientists. Our examples from biology and the environmental sciences use HTCondor, an open source HTC system

Detection of silver carp DNA from water in contact with a silver carp carcass.

<p>A plus (+) indicates a positive detection of silver carp DNA over time among triplicate water samples from chambers containing a juvenile silver carp carcass. A minus (−) indicates no detection of silver carp DNA.</p><p>Detection of silver carp DNA from water in contact with a silver carp carcass.</p

Detection of silver carp DNA from slime adhering to metal trays.

<p>A plus (+) indicates a positive detection of silver carp DNA over time among triplicate swabs from silver carp slime accumulated on metal trays. A minus (−) indicates no detection of silver carp DNA. NA indicates discarded data due to contamination detected in extraction negative controls.</p><p>Detection of silver carp DNA from slime adhering to metal trays.</p

Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency

Summary: Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore, we increased the efficiency with a combination of epigenomic modifiers and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial, and early pluripotency genes can be triggered independently such that any combination of these events can occur in single cells. Sustained co-expression of Epcam, Nanog, and Sox2 with other genes is required to progress toward iPSCs. Ehf, Phlda2, and translation initiation factor Eif4a1 play functional roles in robust iPSC generation. Using regulatory network analysis, we identify a critical role for signaling inhibition by 2i in repressing somatic expression and synergy between the epigenomic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation. : Tran et al. combine ascorbic acid, 2i, and Dot1l inhibition to robustly generate induced pluripotent stem cells. With single-cell transcriptomes, they define the transcriptional signature and key regulators of reprogramming cells. Using network analysis, they find 2i suppresses somatic while ascorbic acid and Dot1l inhibitor collaboratively upregulate pluripotency genes

Genetic Analysis Shows that Morphology Alone Cannot Distinguish Asian Carp Eggs from Those of Other Cyprinid Species

<p>Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular methods to determine species identity. Genetic identification using the cytochrome-<i>c</i> oxidase 1 gene was attempted for a total of 41 eggs. Due to the preservation technique used (formalin) and the resulting DNA degradation, sequences were recovered from only 17 individual eggs. In all 17 cases, cyprinids other than Asian carp (usually <i>Notropis</i> sp.) were identified as the most likely species. In previously published reports, a key characteristic that distinguished Asian carp eggs from those of other cyprinids was size: Asian carp eggs exhibited diameters ranging from 4.0 to 6.0 mm and were thought to be much larger than the otherwise similar eggs of native species. Eggs from endemic cyprinids were believed to rarely reach 3.0 mm and had not been observed to exceed 3.3 mm. However, many of the eggs that were genetically identified as originating from native cyprinids were as large as 4.0 mm in diameter (at early developmental stages) and were therefore large enough to overlap with the lower end of the size range observed for Asian carp eggs. Researchers studying the egg stages of Asian carp and other cyprinids should plan on preserving subsets of eggs for genetic analysis to confirm morphological identifications.</p> <p>Received July 30, 2015; accepted April 22, 2016 Published online August 31, 2016 </p

The role of conservation agriculture in sustainable agriculture

The paper focuses on conservation agriculture (CA), defined as minimal soil disturbance (no-till, NT) and permanent soil cover (mulch) combined with rotations, as a more sustainable cultivation system for the future. Cultivation and tillage play an important role in agriculture. The benefits of tillage in agriculture are explored before introducing conservation tillage (CT), a practice that was borne out of the American dust bowl of the 1930s. The paper then describes the benefits of CA, a suggested improvement on CT, where NT, mulch and rotations significantly improve soil properties and other biotic factors. The paper concludes that CA is a more sustainable and environmentally friendly management system for cultivating crops. Case studies from the rice–wheat areas of the Indo-Gangetic Plains of South Asia and the irrigated maize–wheat systems of Northwest Mexico are used to describe how CA practices have been used in these two environments to raise production sustainably and profitably. Benefits in terms of greenhouse gas emissions and their effect on global warming are also discussed. The paper concludes that agriculture in the next decade will have to sustainably produce more food from less land through more efficient use of natural resources and with minimal impact on the environment in order to meet growing population demands. Promoting and adopting CA management systems can help meet this goal