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1.
Ecol Appl ; 33(4): e2834, 2023 06.
Article in English | MEDLINE | ID: mdl-36864737

ABSTRACT

Restoration in dryland ecosystems often has poor success due to low and variable water availability, degraded soil conditions, and slow plant community recovery rates. Restoration treatments can mitigate these constraints but, because treatments and subsequent monitoring are typically limited in space and time, our understanding of their applicability across broader environmental gradients remains limited. To address this limitation, we implemented and monitored a standardized set of seeding and soil surface treatments (pits, mulch, and ConMod artificial nurse plants) designed to enhance soil moisture and seedling establishment across RestoreNet, a growing network of 21 diverse dryland restoration sites in the southwestern USA over 3 years. Generally, we found that the timing of precipitation relative to seeding and the use of soil surface treatments were more important in determining seeded species emergence, survival, and growth than site-specific characteristics. Using soil surface treatments in tandem with seeding promoted up to 3× greater seedling emergence densities compared with seeding alone. The positive effect of soil surface treatments became more prominent with increased cumulative precipitation since seeding. The seed mix type with species currently found within or near a site and adapted to the historical climate promoted greater seedling emergence densities compared with the seed mix type with species from warmer, drier conditions expected to perform well under climate change. Seed mix and soil surface treatments had a diminishing effect as plants developed beyond the first season of establishment. However, we found strong effects of the initial period seeded and of the precipitation leading up to each monitoring date on seedling survival over time, especially for annual and perennial forbs. The presence of exotic species exerted a negative influence on seedling survival and growth, but not initial emergence. Our findings suggest that seeded species recruitment across drylands can generally be promoted, regardless of location, by (1) incorporation of soil surface treatments, (2) employment of near-term seasonal climate forecasts, (3) suppression of exotic species, and (4) seeding at multiple times. Taken together, these results point to a multifaceted approach to ameliorate harsh environmental conditions for improved seeding success in drylands, both now and under expected aridification.


Subject(s)
Ecosystem , Soil , Seedlings , Plants , Seeds
2.
Genome Res ; 28(6): 836-845, 2018 06.
Article in English | MEDLINE | ID: mdl-29728366

ABSTRACT

Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of an SVA retrotransposon reporter. By using naïve versus primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development. Although the HUSH component FAM208A binds to endogenous retroviruses (ERVs) and long interspersed element-1s (LINE-1s or L1s), it is mainly required to repress evolutionarily young L1s (mouse-specific lineages <5 million years old). TRIM28, in contrast, is necessary to repress both ERVs and young L1s. Genes co-repressed by TRIM28 and FAM208A are evolutionarily young, or exhibit tissue-specific expression, are enriched in young L1s, and display evidence for regulation through LTR promoters. Finally, we demonstrate that the HUSH complex is also required to repress L1 elements in human cells. Overall, these data indicate that the HUSH complex and TRIM28 co-repress young retrotransposons and new genes rewired by retrotransposon noncoding DNA.


Subject(s)
Genome, Human , Nuclear Proteins/genetics , Retroelements/genetics , Tripartite Motif-Containing Protein 28/genetics , Animals , DNA Methylation/genetics , Endogenous Retroviruses/genetics , Heterochromatin/genetics , Humans , Long Interspersed Nucleotide Elements/genetics , Mice , Promoter Regions, Genetic
3.
EMBO Rep ; 20(12): e49262, 2019 12 05.
Article in English | MEDLINE | ID: mdl-31621182

ABSTRACT

Transposon silencing requires the histone methyltransferase SETDB1. In this issue of EMBO Reports, Tsusaka et al [1] and Osumi et al [2] illustrate how the cofactor ATF7IP and its fly homolog Windei (Wde) regulate the methyltransferase function of SETDB1 through its nuclear licensing. The new insight gained from these two articles will shift how we think about epigenetic regulation and its multiple layers of control.


Subject(s)
Cell Nucleus , Epigenesis, Genetic , Ubiquitination
4.
Proc Natl Acad Sci U S A ; 115(15): E3529-E3538, 2018 04 10.
Article in English | MEDLINE | ID: mdl-29581310

ABSTRACT

Adeno-associated virus (AAV) is a small human Dependovirus whose low immunogenicity and capacity for long-term persistence have led to its widespread use as vector for gene therapy. Despite great recent successes in AAV-based gene therapy, further improvements in vector technology may be hindered by an inadequate understanding of various aspects of basic AAV biology. AAV is unique in that its replication is largely dependent on a helper virus and cellular factors. In the absence of helper virus coinfection, wild-type AAV establishes latency through mechanisms that are not yet fully understood. Challenging the currently held model for AAV latency, we show here that the corepressor Krüppel-associated box domain-associated protein 1 (KAP1) binds the latent AAV2 genome at the rep ORF, leading to trimethylation of AAV2-associated histone 3 lysine 9 and that the inactivation of KAP1 repression is necessary for AAV2 reactivation and replication. We identify a viral mechanism for the counteraction of KAP1 in which interference with the KAP1 phosphatase protein phosphatase 1 (PP1) by the AAV2 Rep proteins mediates enhanced phosphorylation of KAP1-S824 and thus relief from KAP1 repression. Furthermore, we show that this phenomenon involves recruitment of the NIPP1 (nuclear inhibitor of PP1)-PP1α holoenzyme to KAP1 in a manner dependent upon the NIPP1 FHA domain, identifying NIPP1 as an interaction partner for KAP1 and shedding light on the mechanism through which PP1 regulates cellular KAP1 activity.


Subject(s)
DNA-Binding Proteins/metabolism , Dependovirus/metabolism , Receptors, Neuropeptide Y/antagonists & inhibitors , Tripartite Motif-Containing Protein 28/metabolism , Viral Proteins/metabolism , Cell Line , DNA Replication/physiology , DNA, Viral/genetics , DNA-Binding Proteins/genetics , Dependovirus/genetics , Epigenesis, Genetic , Genome, Viral , HEK293 Cells , HeLa Cells , Humans , Parvoviridae Infections/metabolism , Parvoviridae Infections/virology , Receptors, Neuropeptide Y/metabolism , Viral Proteins/genetics , Virion/metabolism , Virus Latency , Virus Replication/physiology
5.
EMBO Rep ; 19(10)2018 10.
Article in English | MEDLINE | ID: mdl-30061100

ABSTRACT

Endogenous retroviruses (ERVs) have accumulated in vertebrate genomes and contribute to the complexity of gene regulation. KAP1 represses ERVs during development by its recruitment to their repetitive sequences through KRAB zinc-finger proteins (KZNFs), but little is known about the regulation of ERVs in adult tissues. We observed that KAP1 repression of HERVK14C was conserved in differentiated human cells and performed KAP1 knockout to obtain an overview of KAP1 function. Our results show that KAP1 represses ERVs (including HERV-T and HERV-S) and ZNF genes, both of which overlap with KAP1 binding sites and H3K9me3 in multiple cell types. Furthermore, this pathway is functionally conserved in adult human peripheral blood mononuclear cells. Cytosine methylation that acts on KAP1 regulated loci is necessary to prevent an interferon response, and KAP1-depletion leads to activation of some interferon-stimulated genes. Finally, loss of KAP1 leads to a decrease in H3K9me3 enrichment at ERVs and ZNF genes and an RNA-sensing response mediated through MAVS signaling. These data indicate that the KAP1-KZNF pathway contributes to genome stability and innate immune control in adult human cells.


Subject(s)
Endogenous Retroviruses/genetics , Immunity, Innate/genetics , Repressor Proteins/genetics , Tripartite Motif-Containing Protein 28/genetics , Binding Sites/genetics , DNA Methylation/genetics , Endogenous Retroviruses/immunology , Endogenous Retroviruses/pathogenicity , Gene Expression Regulation/immunology , Gene Knockout Techniques , Genome, Human/immunology , Histones/genetics , Histones/immunology , Humans , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/virology , Promoter Regions, Genetic
6.
Nature ; 487(7405): 57-63, 2012 Jul 05.
Article in English | MEDLINE | ID: mdl-22722858

ABSTRACT

Embryonic stem (ES) cells are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass, which lacks the ability to produce all extraembryonic tissues. Here we identify a rare transient cell population within mouse ES and induced pluripotent stem (iPS) cell cultures that expresses high levels of transcripts found in two-cell (2C) embryos in which the blastomeres are totipotent. We genetically tagged these 2C-like ES cells and show that they lack the inner cell mass pluripotency proteins Oct4 (also known as Pou5f1), Sox2 and Nanog, and have acquired the ability to contribute to both embryonic and extraembryonic tissues. We show that nearly all ES cells cycle in and out of this privileged state, which is partially controlled by histone-modifying enzymes. Transcriptome sequencing and bioinformatic analyses showed that many 2C transcripts are initiated from long terminal repeats derived from endogenous retroviruses, suggesting this foreign sequence has helped to drive cell-fate regulation in placental mammals.


Subject(s)
Cell Dedifferentiation/genetics , Embryonic Stem Cells/cytology , Embryonic Stem Cells/metabolism , Endogenous Retroviruses/genetics , Pluripotent Stem Cells/cytology , Totipotent Stem Cells/cytology , Totipotent Stem Cells/metabolism , Animals , Cell Dedifferentiation/physiology , Cell Lineage/genetics , Chimera/embryology , Chromatin/genetics , Chromatin/metabolism , Embryo, Mammalian/cytology , Embryo, Mammalian/metabolism , Embryo, Mammalian/virology , Embryonic Stem Cells/virology , Epigenesis, Genetic , Female , Gene Expression Regulation, Developmental , Genes, Reporter/genetics , Histones/chemistry , Histones/metabolism , Induced Pluripotent Stem Cells/cytology , Induced Pluripotent Stem Cells/metabolism , Lysine/chemistry , Lysine/metabolism , Methylation , Mice , Phenotype , Pluripotent Stem Cells/metabolism , Pluripotent Stem Cells/virology , Terminal Repeat Sequences/genetics , Totipotent Stem Cells/virology , Transcriptome/genetics
7.
J Environ Manage ; 207: 292-302, 2018 Feb 01.
Article in English | MEDLINE | ID: mdl-29182976

ABSTRACT

As recreational visitation to the Sonoran Desert increases, the concern of scientists, managers and advocates who manage its natural resources deepens. Although many studies have been conducted on trampling of undisturbed vegetation and the effects of trails on adjacent plant and soil communities, little such research has been conducted in the arid southwest. We sampled nine 450-m trail segments with different visitation levels in Scottsdale's McDowell Sonoran Preserve over three years to understand the effects of visitation on soil erosion, trailside soil crusts and plant communities. Soil crust was reduced by 27-34% near medium and high use trails (an estimated peak rate of 13-70 visitors per hour) compared with control plots, but there was less than 1% reduction near low use trails (peak rate of two to four visitors per hour). We did not detect soil erosion in the center 80% of the trampled area of any of the trails. The number of perennial plant species dropped by less than one plant species on average, but perennial plant cover decreased by 7.5% in trailside plots compared with control plots 6 m off-trail. At the current levels of visitation, the primary management focus should be keeping people on the originally constructed trail tread surface to reduce impact to adjacent soil crusts.


Subject(s)
Conservation of Natural Resources , Desert Climate , Recreation , Ecosystem , Natural Resources , Plants , Soil
8.
Genome Res ; 24(8): 1251-9, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24879558

ABSTRACT

Endogenous retroelements (EREs) account for about half of the mouse or human genome, and their potential as insertional mutagens and transcriptional perturbators is suppressed by early embryonic epigenetic silencing. Here, we asked how ERE control is maintained during the generation of induced pluripotent stem cells (iPSCs), as this procedure involves profound epigenetic remodeling. We found that all EREs tested were markedly up-regulated during the reprogramming of either mouse embryonic fibroblasts, human CD34(+) cells, or human primary hepatocytes. At the iPSC stage, EREs of some classes were repressed, whereas others remained highly expressed, yielding a pattern somewhat reminiscent of that recorded in embryonic stem cells. However, variability persisted between individual iPSC clones in the control of specific ERE integrants. Both during reprogramming and in iPS cells, the up-regulation of specific EREs significantly impacted on the transcription of nearby cellular genes. While transcription triggered by specific ERE integrants at highly precise developmental stages may be an essential step toward obtaining pluripotent cells, the broad and unspecific unleashing of the repetitive genome observed here may contribute to the inefficiency of the reprogramming process and to the phenotypic heterogeneity of iPSCs.


Subject(s)
Endogenous Retroviruses/genetics , Induced Pluripotent Stem Cells/physiology , Transcriptome , Animals , Cells, Cultured , Cellular Reprogramming , Gene Silencing , Humans , Mice , Up-Regulation
9.
Genome Res ; 23(3): 452-61, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23233547

ABSTRACT

TRIM28 is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced by histone modifications typical of active enhancers, stimulating transcription of nearby cellular genes, notably those harboring bivalent promoters. Correspondingly, ERV-derived sequences can repress or enhance expression from an adjacent promoter in transgenic embryos depending on their TRIM28 sensitivity in ES cells. TRIM28-mediated control of ERVs is therefore crucial not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos.


Subject(s)
Embryonic Stem Cells/metabolism , Nuclear Proteins/metabolism , Repressor Proteins/metabolism , Retroelements , Transcription, Genetic , Animals , Chromatin/genetics , Chromatin/metabolism , Chromosome Mapping , DNA Methylation , Embryonic Stem Cells/cytology , Embryonic Stem Cells/virology , Endogenous Retroviruses/genetics , Gene Deletion , Gene Expression Regulation, Developmental , Gene Silencing , Genetic Loci , Histones/genetics , Histones/metabolism , Mice , Nuclear Proteins/genetics , Promoter Regions, Genetic , Repressor Proteins/genetics , Sequence Analysis, RNA , Tripartite Motif-Containing Protein 28 , Up-Regulation
10.
Development ; 140(3): 519-29, 2013 Feb 01.
Article in English | MEDLINE | ID: mdl-23293284

ABSTRACT

Endogenous retroviruses (ERVs) undergo de novo DNA methylation during the first few days of mammalian embryogenesis, although the factors that control the targeting of this process are largely unknown. We asked whether KAP1 (KRAB-associated protein 1) is involved in this mechanism because of its previously defined role in maintaining the silencing of ERVs through the histone methyltransferase ESET and histone H3 lysine 9 trimethylation. Here, we demonstrate that introduced ERV sequences are sufficient to direct rapid de novo methylation of a flanked promoter in embryonic stem (ES) cells. This mechanism requires the presence of an ERV sequence-recognizing KRAB zinc-finger protein (ZFP) and both KAP1 and ESET. Furthermore, this process can also take place on a strong cellular promoter and leads to methylation signatures that are subsequently maintained in vivo throughout embryogenesis. Finally, we show that methylation of ERVs residing in the genome is affected by knockout of KAP1 in early embryos. KRAB-ZFPs, KAP1 and ESET are thus likely to be responsible for the early embryonic instatement of stable epigenetic marks at ERV-containing loci.


Subject(s)
DNA Methylation , DNA, Viral/metabolism , Endogenous Retroviruses/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Nuclear Proteins/metabolism , Repressor Proteins/metabolism , Animals , Animals, Genetically Modified , DNA, Viral/genetics , Embryo, Mammalian/cytology , Embryo, Mammalian/metabolism , Embryo, Mammalian/virology , Embryonic Stem Cells/cytology , Embryonic Stem Cells/metabolism , Embryonic Stem Cells/virology , Endogenous Retroviruses/enzymology , Endogenous Retroviruses/genetics , Gene Expression Regulation, Developmental , Gene Knockout Techniques , Gene Silencing , Gene Transfer Techniques , Genetic Vectors/genetics , Genetic Vectors/metabolism , HEK293 Cells , Histone-Lysine N-Methyltransferase/genetics , Histones/genetics , Histones/metabolism , Humans , Lentivirus/genetics , Lentivirus/metabolism , Mice , Nuclear Proteins/genetics , Promoter Regions, Genetic , Repressor Proteins/genetics , Transcriptome , Transfection , Tripartite Motif-Containing Protein 28
11.
Nature ; 463(7278): 237-40, 2010 Jan 14.
Article in English | MEDLINE | ID: mdl-20075919

ABSTRACT

More than forty per cent of the mammalian genome is derived from retroelements, of which about one-quarter are endogenous retroviruses (ERVs). Some are still active, notably in mice the highly polymorphic early transposon (ETn)/MusD and intracisternal A-type particles (IAP). ERVs are transcriptionally silenced during early embryogenesis by histone and DNA methylation (and reviewed in ref. 7), although the initiators of this process, which is essential to protect genome integrity, remain largely unknown. KAP1 (KRAB-associated protein 1, also known as tripartite motif-containing protein 28, TRIM28) represses genes by recruiting the histone methyltransferase SETDB1, heterochromatin protein 1 (HP1) and the NuRD histone deacetylase complex, but few of its physiological targets are known. Two lines of evidence suggest that KAP1-mediated repression could contribute to the control of ERVs: first, KAP1 can trigger permanent gene silencing during early embryogenesis, and second, a KAP1 complex silences the retrovirus murine leukaemia virus in embryonic cells. Consistent with this hypothesis, here we show that KAP1 deletion leads to a marked upregulation of a range of ERVs, in particular IAP elements, in mouse embryonic stem (ES) cells and in early embryos. We further demonstrate that KAP1 acts synergistically with DNA methylation to silence IAP elements, and that it is enriched at the 5' untranslated region (5'UTR) of IAP genomes, where KAP1 deletion leads to the loss of histone 3 lysine 9 trimethylation (H3K9me3), a hallmark of KAP1-mediated repression. Correspondingly, IAP 5'UTR sequences can impose in cis KAP1-dependent repression on a heterologous promoter in ES cells. Our results establish that KAP1 controls endogenous retroelements during early embryonic development.


Subject(s)
Embryonic Stem Cells/metabolism , Endogenous Retroviruses/genetics , Gene Silencing , Genes, Intracisternal A-Particle/genetics , Nuclear Proteins/metabolism , Repressor Proteins/metabolism , 5' Untranslated Regions/genetics , Acetylation , Animals , DNA Methylation , Embryo, Mammalian/metabolism , Embryo, Mammalian/virology , Embryonic Stem Cells/virology , Fibroblasts , Genes, Reporter , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Histones/metabolism , Leukemia Virus, Murine/genetics , Leukemia Virus, Murine/physiology , Lysine/metabolism , Methylation , Mice , Nuclear Proteins/deficiency , Nuclear Proteins/genetics , Promoter Regions, Genetic/genetics , Repressor Proteins/deficiency , Repressor Proteins/genetics , Tripartite Motif-Containing Protein 28
12.
Retrovirology ; 12: 45, 2015 May 29.
Article in English | MEDLINE | ID: mdl-26021318

ABSTRACT

Over half of our genome is composed of retrotransposons, which are mobile elements that can readily amplify their copy number by replicating through an RNA intermediate. Most of these elements are no longer mobile but still contain regulatory sequences that can serve as promoters, enhancers or repressors for cellular genes. Despite dominating our genetic content, little is known about the precise functions of retrotransposons, which include both endogenous retroviruses (ERVs) and non-LTR elements like long interspersed nuclear element 1 (LINE-1). However, a few recent cutting-edge publications have illustrated how retrotransposons shape species-specific stem cell gene expression by two opposing mechanisms, involving their recruitment of stem cell-enriched transcription factors (TFs): firstly, they can activate expression of genes linked to naïve pluripotency, and secondly, they can induce repression of proximal genes. The paradox that different retrotransposons are active or silent in embryonic stem cells (ESCs) can be explained by differences between retrotransposon families, between individual copies within the same family, and between subpopulations of ESCs. Since they have coevolved with their host genomes, some of them have been co-opted to perform species-specific beneficial functions, while others have been implicated in genetic disease. In this review, we will discuss retrotransposon functions in ESCs, focusing on recent mechanistic advances of how HERV-H has been adopted to preserve human naïve pluripotency and how particular LINE-1, SVA and ERV family members recruit species-specific transcriptional repressors. This review highlights the fine balance between activation and repression of retrotransposons that exists to harness their ability to drive evolution, while minimizing the risk they pose to genome integrity.


Subject(s)
Embryonic Stem Cells/physiology , Gene Expression Regulation , Retroelements , Humans
13.
PLoS One ; 19(4): e0297227, 2024.
Article in English | MEDLINE | ID: mdl-38635739

ABSTRACT

Preservation of undeveloped land near urban areas is a common conservation practice. However, ecological processes may still be affected by adjacent anthropogenic activities. Ground-dwelling arthropods are a diverse group of organisms that are critical to ecological processes such as nutrient cycling, which are sensitive to anthropogenic activities. Here, we study arthropod dynamics in a preserve located in a heavily urbanized part of the Sonoran Desert, Arizona, U.S.. We compared arthropod biodiversity and community composition at ten locations, four paired sites representing the urban edge and one pair in the Preserve interior. In total, we captured and identified 25,477 arthropod individuals belonging to 287 lowest practical taxa (LPT) over eight years of sampling. This included 192 LPTs shared between interior and edge sites, with 44 LPTs occurring exclusively in interior sites and 48 LPTs occurring exclusively in edge sites. We found two site pairs had higher arthropod richness on the preserve interior, but results for evenness were mixed among site pairs. Compositionally, the interior and edge sites were more than 40% dissimilar, driven by species turnover. Importantly, we found that some differences were only apparent seasonally; for example edge sites had more fire ants than interior sites only during the summer. We also found that temperature and precipitation were strong predictors of arthropod composition. Our study highlights that climate can interact with urban edge effects on arthropod biodiversity.


Subject(s)
Arthropods , Humans , Animals , Arizona , Climate , Biodiversity , Seasons , Ecosystem , Desert Climate
14.
Ecol Appl ; 23(7): 1554-73, 2013 Oct.
Article in English | MEDLINE | ID: mdl-24261040

ABSTRACT

The control of agricultural pests is an important ecosystem service provided by predacious insects. In Midwestern USA, areas of remnant tallgrass prairie and prairie restorations may serve as relatively undisturbed sources of natural predators, and smaller areas of non-crop habitats such as seminatural areas and conservation plantings (CP) may serve as stepping stones across landscapes dominated by intensive agriculture. However, little is known about the flow of beneficial insects across large habitat networks. We measured abundance of soybean aphids and predators in 15 CP and adjacent soybean fields. We tested two hypotheses: (1) landscape connectivity enhances the flow of beneficial insects; and (2) prairies act as a source of sustaining populations of beneficial insects in well-connected habitats, by using adaptations of graph and circuit theory, respectively. For graph connectivity, incoming fluxes to the 15 CP from connected habitats were measured using an area- and distance-weighted flux metric with a range of negative exponential dispersal kernels. Distance was weighted by the percentage of seminatural area within ellipse-shaped landscapes, the shape of which was determined with correlated random walks. For circuit connectivity, effective conductance from the prairie to the individual 15 CP was measured by regarding the flux as conductance in a circuit. We used these two connectivity measures to predict the abundance of natural enemies in the selected sites. The most abundant predators were Anthocoridae, followed by exotic Coccinellidae, and native Coccinellidae. Predator abundances were explained well by aphid abundance. However, only native Coccinellidae were influenced by the flux and conductance. Interestingly, exotic Coccinellidae were negatively related to the flux, and native Coccinellidae were highly influenced by the interaction between exotic Coccinellidae and aphids. Our area- and distance-weighted flux and the conductance variables showed better fit to field data than area-weighted flux or Euclidean distance from the prairie. These results indicate that the network of seminatural areas has greater influence on the flow of native predators than that of exotic predators, and that the prairie acts as a source for native Coccinellidae. Managers can enhance conservation biocontrol and sustain the diversity of natural enemies by optimizing habitat networks.


Subject(s)
Biological Control Agents , Conservation of Natural Resources/methods , Models, Biological , Pest Control, Biological , Animals , Ecosystem , Indiana , Insecta , Midwestern United States , Predatory Behavior
15.
Insects ; 15(1)2023 Dec 21.
Article in English | MEDLINE | ID: mdl-38276819

ABSTRACT

Butterfly populations are declining worldwide, reflecting our current global biodiversity crisis. Because butterflies are a popular and accurate indicator of insect populations, these declines reflect an even more widespread threat to insects and the food webs upon which they rely. As small ectotherms, insects have a narrow range of habitable conditions; hence, extreme fluctuations and shifts caused by climate change may increase insects' risk of extinction. We evaluated trends of butterfly richness and abundance and their relationship with relevant climate variables in Arizona, U.S.A., using the past 40 years of community science data. We focused on precipitation and temperature as they are known to be influential for insect survival, particularly in arid areas like southwestern U.S.A. We found that preceding winter precipitation is a driver of both spring and summer/fall butterfly richness and spring butterfly abundance. In contrast, summer/fall butterfly abundance was driven by summer monsoon precipitations. The statistically significant declines over the 40-year period were summer/fall butterfly abundance and spring butterfly richness. When controlling for the other variables in the model, there was an average annual 1.81% decline in summer/fall season butterfly abundance and an average annual decline of 2.13 species in the spring season. As climate change continues to negatively impact winter precipitation patterns in this arid region, we anticipate the loss of butterfly species in this region and must consider individual butterfly species trends and additional management and conservation needs.

16.
Cell Rep ; 42(6): 112625, 2023 06 27.
Article in English | MEDLINE | ID: mdl-37294634

ABSTRACT

Endogenous retroviruses (ERVs) have rewired host gene networks. To explore the origins of co-option, we employed an active murine ERV, IAPEz, and an embryonic stem cell (ESC) to neural progenitor cell (NPC) differentiation model. Transcriptional silencing via TRIM28 maps to a 190 bp sequence encoding the intracisternal A-type particle (IAP) signal peptide, which confers retrotransposition activity. A subset of "escapee" IAPs (∼15%) exhibits significant genetic divergence from this sequence. Canonical repressed IAPs succumb to a previously undocumented demarcation by H3K9me3 and H3K27me3 in NPCs. Escapee IAPs, in contrast, evade repression in both cell types, resulting in their transcriptional derepression, particularly in NPCs. We validate the enhancer function of a 47 bp sequence within the U3 region of the long terminal repeat (LTR) and show that escapee IAPs convey an activating effect on nearby neural genes. In sum, co-opted ERVs stem from genetic escapees that have lost vital sequences required for both TRIM28 restriction and autonomous retrotransposition.


Subject(s)
Endogenous Retroviruses , Tripartite Motif-Containing Protein 28 , Animals , Mice , Cell Differentiation , Embryonic Stem Cells/metabolism , Endogenous Retroviruses/genetics , Endogenous Retroviruses/metabolism , Histones/metabolism , Tripartite Motif-Containing Protein 28/metabolism , Terminal Repeat Sequences/genetics
17.
Sci Adv ; 8(43): eabp8085, 2022 Oct 28.
Article in English | MEDLINE | ID: mdl-36306355

ABSTRACT

Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.


Subject(s)
DNA, Satellite , Repressor Proteins , Animals , Mice , DNA, Satellite/genetics , Mammals/genetics , Oligonucleotide Array Sequence Analysis , Repressor Proteins/metabolism , Transcription Factors/genetics , Chromosomes
18.
Ecology ; 103(10): e3775, 2022 10.
Article in English | MEDLINE | ID: mdl-35661139

ABSTRACT

Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals, but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here we present the data from Snapshot USA 2020, a second annual national mammal survey of the USA. This project involved 152 scientists setting camera traps in a standardized protocol at 1485 locations across 103 arrays in 43 states for a total of 52,710 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in 2 years that includes data from both during and before the COVID-19 pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total, we recorded 117,415 detections of 78 species of wild mammals, 9236 detections of at least 43 species of birds, 15,851 detections of six domestic animals and 23,825 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences among years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.


Subject(s)
COVID-19 , Animals , Animals, Wild , Birds , COVID-19/epidemiology , Humans , Mammals , Pandemics , United States
19.
Ecology ; 102(6): e03353, 2021 06.
Article in English | MEDLINE | ID: mdl-33793977

ABSTRACT

With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August-24 November of 2019). We sampled wildlife at 1,509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the United States. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as will future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.


Subject(s)
Animals, Wild , Mammals , Animals , Birds , Population Dynamics , United States
20.
J Virol ; 83(4): 1555-62, 2009 Feb.
Article in English | MEDLINE | ID: mdl-19036811

ABSTRACT

Lentiviral vectors deliver antigens to dendritic cells (DCs) in vivo, but they do not trigger DC maturation. We therefore expressed a viral protein that constitutively activates NF-kappaB, vFLIP from Kaposi's sarcoma-associated herpesvirus (KSHV), in a lentivector to mature DCs. vFLIP activated NF-kappaB in mouse bone marrow-derived DCs in vitro and matured these DCs to a similar extent as lipopolysaccharide; costimulatory markers CD80, CD86, CD40, and ICAM-1 were upregulated and tumor necrosis factor alpha and interleukin-12 secreted. The vFLIP-expressing lentivector also matured DCs in vivo. When we coexpressed vFLIP in a lentivector with ovalbumin (Ova), we found an increased immune response to Ova; up to 10 times more Ova-specific CD8(+) T cells secreting gamma interferon were detected in the spleens of vFLIP_Ova-immunized mice than in the spleens of mice immunized with GFP_Ova. Furthermore, this increased CD8(+) T-cell response correlated with improved tumor-free survival in a tumor therapy model. A single immunization with vFLIP_Ova also reduced the parasite load when mice were challenged with OVA-Leishmania donovani. In conclusion, vFLIP from KSHV is a DC activator, maturing DCs in vitro and in vivo. This demonstrates that NF-kappaB activation is sufficient to induce many aspects of DC maturation and that expression of a constitutive NF-kappaB activator can improve the efficacy of a vaccine vector.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Dendritic Cells/virology , Lentivirus/genetics , NF-kappa B/biosynthesis , Viral Proteins/immunology , Viral Vaccines/genetics , Animals , Cancer Vaccines/immunology , Cytokines/biosynthesis , Leishmania donovani/immunology , Leishmaniasis/prevention & control , Lentivirus/immunology , Mice , Neoplasms/immunology , Ovalbumin/immunology , Receptors, Immunologic/biosynthesis , Spleen/immunology , Survival Analysis , Viral Proteins/genetics , Viral Vaccines/immunology
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