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"Lynch, Michael J"
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Defining crime : a critique of the concept and its implication
\"Defining Crime explores the limitations of the legal definition of crime, how that politically based definition has shaped criminological research, and why criminologists must redefine crime to include scientific objectivity. Lynch, Stretesky, and Long argue that a scientific definition of crime must be detached from criminal law and the variation the political construction imposes. The authors propose an alternative definition of crime, explore its limitations, and how it can reshape criminological research. \"-- Provided by publisher.
Book
Ecology and exploration of the rare biosphere
Key Points
Microbial-community abundance distributions have a long 'tail' of low-abundance organisms, referred to as the rare biosphere, which often comprises the large majority of species.
Rare-biosphere microorganisms display specific and sometimes unique ecology and biogeography that can differ substantially from that of more abundant representatives.
The rare biosphere contributes to a persistent microbial seed bank, contrasting the influence of local microbial extinction and immigration.
Recruitment from the rare biosphere provides a broad reservoir of ecological function and resiliency (redundancy and flexibility).
Broad time-series studies with rich metadata will improve the study of rare-biosphere dynamics and conditionally rare taxa.
Study of the rare biosphere is prone to experimental artefacts (sequencing noise) and biological artefacts (dormancy and taphonomic gradients).
The majority of microbial diversity exists, at least transiently, in the rare biosphere.
Novel rare-biosphere members can be studied through cultivation, targeted phylogenetic mining and single-cell genomics.
The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. Lynch and Neufeld discuss the ecology of rare microbial populations and highlight molecular and computational methods for targeting taxonomic 'blind spots' in the rare biosphere of complex microbial communities.
The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.
Journal Article
On the geometry of speciesist policing: The federal bureau of investigation's animal cruelty data
This article contests the animal cruelty statistics newly collected and publicized in the US by the Federal Bureau of Investigation (FBI). In what follows, we (1) outline the inclusion of animal cruelty in the FBI's National Incident- Based Reporting System (NIBRS), 2016-2020; (2) analyze trends in animal cruelty cases reported in NIBRS; (3) identify key data validity, methodological and theoretical problems in NIBRS, especially with the FBI's attempt to generate knowledge of the link between animal cruelty and interpersonal violence; and (4) juxtapose the FBI's circumscribed concept of animal cruelty with the much more inclusive circle of compassion advanced by nonspeciesist and green criminology. We challenge illusions that the criminalization of animal cruelty is driven by a logic of benign inevitability, and ponder how the extension of compassion to a few favored species coexists with and even engenders de-civilizing countertrends, such as the immense abuse that occurs worldwide in the animal industrial complex. Therefore, we issue a call for the development of a nonspeciesist research program, both monocultural and cross-cultural, into the dynamics of the policing and surveillance of animal cruelty and animal abuse in a broad range of societies.
Journal Article
Green criminology : crime, justice and the environment
\"This book provides an overview and assessment of green criminology. Based on a political-economic analysis, Green Criminology draws attention to the ways in which the political-economic organization of capitalism causes ecological destruction and disorganization. Focusing on real-world impact, chapters include political-economic examinations of ecological withdrawals, ecological additions, toxic towns, wildlife poaching and trafficking, environmental justice, environmental laws, and nongovernment environmental organizations. The book also explores how ecological footprint, planetary boundary analysis, and other scientific research applies to green criminological analysis\"--Provided by publisher.
Book
Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production
Cobalamin (vitamin B
12
) is a complex metabolite and essential cofactor required by many branches of life, including most eukaryotic phytoplankton. Algae and other cobalamin auxotrophs rely on environmental cobalamin supplied from a relatively small set of cobalamin-producing prokaryotic taxa. Although several
Bacteria
have been implicated in cobalamin biosynthesis and associated with algal symbiosis, the involvement of
Archaea
in cobalamin production is poorly understood, especially with respect to the
Thaumarchaeota
. Based on the detection of cobalamin synthesis genes in available thaumarchaeotal genomes, we hypothesized that
Thaumarchaeota
, which are ubiquitous and abundant in aquatic environments, have an important role in cobalamin biosynthesis within global aquatic ecosystems. To test this hypothesis, we examined cobalamin synthesis genes across sequenced thaumarchaeotal genomes and 430 metagenomes from a diverse range of marine, freshwater and hypersaline environments. Our analysis demonstrates that all available thaumarchaeotal genomes possess cobalamin synthesis genes, predominantly from the anaerobic pathway, suggesting widespread genetic capacity for cobalamin synthesis. Furthermore, although bacterial cobalamin genes dominated most surface marine metagenomes, thaumarchaeotal cobalamin genes dominated metagenomes from polar marine environments, increased with depth in marine water columns, and displayed seasonality, with increased winter abundance observed in time-series datasets (e.g., L4 surface water in the English Channel). Our results also suggest niche partitioning between thaumarchaeotal and cyanobacterial ribosomal and cobalamin synthesis genes across all metagenomic datasets analyzed. These results provide strong evidence for specific biogeographical distributions of thaumarchaeotal cobalamin genes, expanding our understanding of the global biogeochemical roles played by
Thaumarchaeota
in aquatic environments.
Journal Article
Writs of habeas corpus for nonhuman primates in the United States and the nonhuman rights project: Legal processes and arguments used to secure nonhuman animal rights
Questions concerning (nonhuman) animal rights have been increasingly addressed within the criminological literature due to growing interest in green criminology. Often within criminology, animal rights issues have been primarily addressed from philosophical standpoints, which omit how animal rights are addressed in more concrete terms through the legal system. This philosophical orientation toward animal rights, while important, has led to a neglect of the ways in which animal rights might be promoted through legal means. This article addresses that latter point by exploring the use of writs of habeas corpus for animals promoted by Steven Wise and the Nonhuman Rights Project (NhRP) in the US. Much of the NhRP's efforts have been devoted to nonhuman primates, and consistent with that approach, this assessment focuses attention on legal efforts to protect nonhuman primates' rights. In addition to NhRP efforts, other possibilities for using the law to obtain rights for animals in the US are examined. While this article focuses on circumstances in the US, several nations employ such writs or similar legal mechanisms.
Journal Article
The Treadmill of Crime
Drawing on the work of Allan Schnaiberg, this book returns political economy to green criminology and examines how the expansion of capitalism shapes environmental law, crime and justice. The book is organized around crimes of ecological withdrawals and ecological additions.
The Treadmill of Crime is written by acclaimed experts on the subject of green criminology and examines issues such as the crime in the energy sector as well as the release of toxic waste into the environment and its impact on ecosystems. This book also sets a new research agenda by highlighting problems of ecological disorganization for animal abuse and social disorganization.
This book will be of interest to students, researchers and academics in the fields of criminology, political science, environmental sociology, and natural resources.
eBook
A chemosensory-like histidine kinase is dispensable for chemotaxis in vitro but regulates the virulence of Borrelia burgdorferi through modulating the stability of RpoS
As an enzootic pathogen, the Lyme disease bacterium Borrelia burgdorferi possesses multiple copies of chemotaxis proteins, including two chemotaxis histidine kinases (CHK), CheA 1 and CheA 2 . Our previous study showed that CheA 2 is a genuine CHK that is required for chemotaxis; however, the role of CheA 1 remains mysterious. This report first compares the structural features that differentiate CheA 1 and CheA 2 and then provides evidence to show that CheA 1 is an atypical CHK that controls the virulence of B . burgdorferi through modulating the stability of RpoS, a key transcriptional regulator of the spirochete. First, microscopic analyses using green-fluorescence-protein (GFP) tags reveal that CheA 1 has a unique and dynamic cellular localization. Second, loss-of-function studies indicate that CheA 1 is not required for chemotaxis in vitro despite sharing a high sequence and structural similarity to its counterparts from other bacteria. Third, mouse infection studies using needle inoculations show that a deletion mutant of CheA 1 ( cheA 1 mut ) is able to establish systemic infection in immune-deficient mice but fails to do so in immune-competent mice albeit the mutant can survive at the inoculation site for up to 28 days. Tick and mouse infection studies further demonstrate that CheA 1 is dispensable for tick colonization and acquisition but essential for tick transmission. Lastly, mechanistic studies combining immunoblotting, protein turnover, mutagenesis, and RNA-seq analyses reveal that depletion of CheA 1 affects RpoS stability, leading to reduced expression of several RpoS-regulated virulence factors (i.e., OspC, BBK32, and DbpA), likely due to dysregulated clpX and lon protease expression. Bulk RNA-seq analysis of infected mouse skin tissues further show that cheA 1 mut fails to elicit mouse tnf-α , il-10 , il-1β , and ccl2 expression, four important cytokines for Lyme disease development and B . burgdorferi transmigration. Collectively, these results reveal a unique role and regulatory mechanism of CheA 1 in modulating virulence factor expression and add new insights into understanding the regulatory network of B . burgdorferi .
Journal Article
MCP5, a methyl-accepting chemotaxis protein regulated by both the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, is required for the immune evasion of Borrelia burgdorferi
Borrelia (or Borreliella ) burgdorferi , the causative agent of Lyme disease, is a motile and invasive zoonotic pathogen adept at navigating between its arthropod vector and mammalian host. While motility and chemotaxis are well known to be essential for its enzootic cycle, the role of each methyl-accepting chemotaxis proteins (MCPs) in the infectious cycle of B . burgdorferi remains unclear. In this study, we show that mcp5 , a gene encoding one of the most abundant MCPs in B . burgdorferi , is differentially expressed in response to environmental signals and at distinct stages of the pathogen’s enzootic cycle. Notably, mcp5 expression is regulated by the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, two key regulatory pathways that are critical for the spirochete’s colonization of the tick vector and mammalian host, respectively. Infection experiments with an mcp5 mutant revealed that spirochetes lacking MCP5 were unable to establish infections in either C3H/HeN mice or Severe Combined Immunodeficiency (SCID) mice, which are deficient in adaptive immunity, underscoring MCP5’s critical role in mammalian infection. However, the mcp5 mutant was able to establish infection and disseminate in NOD SCID Gamma (NSG) mice, which are deficient in both adaptive and most innate immune responses, suggesting that MCP5 plays an important role in evading host innate immunity. Moreover, NK cell depletion in C3H and SCID mice restored the infectivity of the mcp5 mutant, further highlighting MCP5’s role in evading NK cell-associated immunity. Co-culture assays with NK cells and macrophages revealed that the mcp5 mutant enhanced interferon-gamma production by NK cells. In the tick vector, the mcp5 mutants survived feeding but failed to transmit to mice. These findings reveal that MCP5, regulated by both the Rrp1 and Rrp2 pathways, is critical for establishing infection in mammalian hosts by evading NK cell-mediated host innate immunity and is important for the transmission of spirochetes from ticks to mammalian hosts. This work provides a foundation for further elucidation of chemotactic signals sensed by MCP5 that facilitate B . burgdorferi in evading host defenses.
Journal Article