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"Patterson, Eric"
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Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance
The human-directed, global selection for glyphosate resistance in weeds has revealed a fascinating diversity of evolved resistance mechanisms, including herbicide sequestration in the vacuole, a rapid cell death response, nucleotide polymorphisms in the herbicide target (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) and increased gene copy number of EPSPS. For this latter mechanism, two distinct molecular genetic mechanisms have been observed, a tandem duplication mechanism and a large extrachromosomal circular DNA (eccDNA) that is tethered to the chromosomes and passed to gametes at meiosis. These divergent mechanisms have a range of consequences for the spread, fitness, and inheritance of resistance traits, and, particularly in the case of the eccDNA, demonstrate how evolved herbicide resistance can generate new insights into plant adaptation to contemporary environmental stress.
Journal Article
The Reagan manifesto : \A time for choosing\ and its influence
\"This book examines how Ronald Reagan's electrifying 1964 televised speech, \"A Time For Choosing,\" ignited the conservative movement within the GOP. Ronald Reagan's televised speech, or what many conservatives today simply call \"The Speech,\" was a call for action, telling Americans that now was \"A Time for Choosing.\" \"The Speech\" catapulted Reagan into national politics, the California governorship, and ultimately the presidency. The themes of the speech, including anti-Communism, strong national defense, and the need to protect the average American from taxes and bureaucracy, ignited the conservative movement in the GOP, resulting over time in the sidelining of the more liberal, establishment wing of the Republican Party. The contributors in this edited volume show how Ronald Reagan's \"coming out\" speech on the national stage helped set the political agenda for the next three decades.\"--Page 4 of cover.
BOOK
Tool use by aquatic animals
Tool-use research has focused primarily on land-based animals, with less consideration given to aquatic animals and the environmental challenges and conditions they face. Here, we review aquatic tool use and examine the contributing ecological, physiological, cognitive and social factors. Tool use among aquatic animals is rare but taxonomically diverse, occurring in fish, cephalopods, mammals, crabs, urchins and possibly gastropods. While additional research is required, the scarcity of tool use can likely be attributable to the characteristics of aquatic habitats, which are generally not conducive to tool use. Nonetheless, studying tool use by aquatic animals provides insights into the conditions that promote and inhibit tool-use behaviour across biomes. Like land-based tool users, aquatic animals tend to find tools on the substrate and use tools during foraging. However, unlike on land, tool users in water often use other animals (and their products) and water itself as a tool. Among sea otters and dolphins, the two aquatic tool users studied in greatest detail, some individuals specialize in tool use, which is vertically socially transmitted possibly because of their long dependency periods. In all, the contrasts between aquatic- and land-based tool users enlighten our understanding of the adaptive value of tool-use behaviour.
Journal Article
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Genomic structural variation (SV) has profound effects on organismal evolution; often serving as a source of novel genetic variation. Gene copy number variation (CNV), one type of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially with environmental stress. Resistance to the widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important grass,
Eleusine indica
(goosegrass); however, the origin and mechanism of these CNVs remain elusive in many weed species due to limited genetic and genomic resources. To study this CNV in goosegrass, we present high-quality reference genomes for glyphosate-susceptible and -resistant goosegrass lines and fine-assembles of the duplication of glyphosate’s target site gene
5-enolpyruvylshikimate-3-phosphate synthase
(
EPSPS
). We reveal a unique rearrangement of
EPSPS
involving chromosome subtelomeres. This discovery adds to the limited knowledge of the importance of subtelomeres as genetic variation generators and provides another unique example for herbicide resistance evolution.
Resistance to herbicide glyphosate can be evolved trough copy number variation (CNV) of its target gene
EPSPS
in goosegrass. Here, the authors assemble the genomes of glyphosate susceptible and resistance lines and provide evidence of sub-telomeric-repeat driven CNV of
EPSPS
could lead to glyphosate resistance.
Journal Article
Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations
Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri S. Watson in 2006, resistant populations have been reported in 28 states. The mechanism of resistance is amplification of a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, and is unique to glyphosate-resistant plants. The replicon contains a single copy of the 10-kb 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene which causes the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. It is not known whether the resistance by this amplification mechanism evolved once and then spread across the country or evolved independently in several locations. To compare genomic representation and variation across the EPSPS replicon, whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. The high sequence conservation among GR biotypes with very few polymorphisms which were widely distributed across the USA further supports the hypothesis that glyphosate resistance most likely originated from a single population. We show that the replicon from different populations was unique to GR plants and had similar levels of amplification.
Journal Article
Specialization in the vicarious learning of novel arbitrary sequences in humans but not orangutans
Sequence learning underlies many uniquely human behaviours, from complex tool use to language and ritual. To understand whether this fundamental cognitive feature is uniquely derived in humans requires a comparative approach. We propose that the vicarious (but not individual) learning of novel arbitrary sequences represents a human cognitive specialization. To test this hypothesis, we compared the abilities of human children aged 3–5 years and orangutans to learn different types of arbitrary sequences (item-based and spatial-based). Sequences could be learned individually (by trial and error) or vicariously from a human (social) demonstrator or a computer (ghost control). We found that both children and orangutans recalled both types of sequence following trial-and-error learning; older children also learned both types of sequence following social and ghost demonstrations. Orangutans' success individually learning arbitrary sequences shows that their failure to do so in some vicarious learning conditions is not owing to general representational problems. These results provide new insights into some of the most persistent discontinuities observed between humans and other great apes in terms of complex tool use, language and ritual, all of which involve the cultural learning of novel arbitrary sequences. This article is part of the theme issue ‘Ritual renaissance: new insights into the most human of behaviours’.
Journal Article
The Ecological Conditions That Favor Tool Use and Innovation in Wild Bottlenose Dolphins (Tursiops sp.)
Dolphins are well known for their exquisite echolocation abilities, which enable them to detect and discriminate prey species and even locate buried prey. While these skills are widely used during foraging, some dolphins use tools to locate and extract prey. In the only known case of tool use in free-ranging cetaceans, a subset of bottlenose dolphins (Tursiops sp.) in Shark Bay, Western Australia habitually employs marine basket sponge tools to locate and ferret prey from the seafloor. While it is clear that sponges protect dolphins' rostra while searching for prey, it is still not known why dolphins probe the substrate at all instead of merely echolocating for buried prey as documented at other sites. By 'sponge foraging' ourselves, we show that these dolphins target prey that both lack swimbladders and burrow in a rubble-littered substrate. Delphinid echolocation and vision are critical for hunting but less effective on such prey. Consequently, if dolphins are to access this burrowing, swimbladderless prey, they must probe the seafloor and in turn benefit from using protective sponges. We suggest that these tools have allowed sponge foraging dolphins to exploit an empty niche inaccessible to their non-tool-using counterparts. Our study identifies the underlying ecological basis of dolphin tool use and strengthens our understanding of the conditions that favor tool use and innovation in the wild.
Journal Article
Elevated vascular transformation blood biomarkers in Long-COVID indicate angiogenesis as a key pathophysiological mechanism
Background
Long-COVID is characterized by prolonged, diffuse symptoms months after acute COVID-19. Accurate diagnosis and targeted therapies for Long-COVID are lacking. We investigated vascular transformation biomarkers in Long-COVID patients.
Methods
A case–control study utilizing Long-COVID patients, one to six months (median 98.5 days) post-infection, with multiplex immunoassay measurement of sixteen blood biomarkers of vascular transformation, including ANG-1, P-SEL, MMP-1, VE-Cad, Syn-1, Endoglin, PECAM-1, VEGF-A, ICAM-1, VLA-4, E-SEL, thrombomodulin, VEGF-R2, VEGF-R3, VCAM-1 and VEGF-D.
Results
Fourteen vasculature transformation blood biomarkers were significantly elevated in Long-COVID outpatients, versus acutely ill COVID-19 inpatients and healthy controls subjects (P < 0.05). A unique two biomarker profile consisting of ANG-1/P-SEL was developed with machine learning, providing a classification accuracy for Long-COVID status of 96%. Individually, ANG-1 and P-SEL had excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, P < 0.0001; validated in a secondary cohort). Specific to Long-COVID, ANG-1 levels were associated with female sex and a lack of disease interventions at follow-up (P < 0.05).
Conclusions
Long-COVID patients suffer prolonged, diffuse symptoms and poorer health. Vascular transformation blood biomarkers were significantly elevated in Long-COVID, with angiogenesis markers (ANG-1/P-SEL) providing classification accuracy of 96%. Vascular transformation blood biomarkers hold potential for diagnostics, and modulators of angiogenesis may have therapeutic efficacy.
Journal Article
Endothelial Glycocalyx Degradation in Critical Illness and Injury
The endothelial glycocalyx is a gel-like layer on the luminal side of blood vessels that is composed of glycosaminoglycans and the proteins that tether them to the plasma membrane. Interest in its properties and function has grown, particularly in the last decade, as its importance to endothelial barrier function has come to light. Endothelial glycocalyx studies have revealed that many critical illnesses result in its degradation or removal, contributing to endothelial dysfunction and barrier break-down. Loss of the endothelial glycocalyx facilitates the direct access of immune cells and deleterious agents (e.g., proteases and reactive oxygen species) to the endothelium, that can then further endothelial cell injury and dysfunction leading to complications such as edema, and thrombosis. Here, we briefly describe the endothelial glycocalyx and the primary components thought to be directly responsible for its degradation. We review recent literature relevant to glycocalyx damage in several critical illnesses (sepsis, COVID-19, trauma and diabetes) that share inflammation as a common denominator with actions by several common agents (hyaluronidases, proteases, reactive oxygen species, etc.). Finally, we briefly cover strategies and therapies that show promise in protecting or helping to rebuild the endothelial glycocalyx such as steroids, protease inhibitors, anticoagulants and resuscitation strategies.
Journal Article