Biology subjects

Vu, J.

Publications and source records attributed to Vu, J..

15 recordsLinked to original sources

bioRxiv2026

Characterization of the frameshift c.515dupC knock-in mouse model of HSPB8-associated myopathy (MFM13) and evaluation of Trehalose as autophagy modulating therapy.

Heat shock protein family B member 8 (HSPB8) is a chaperone involved in the chaperone-assisted selective autophagy (CASA) complex. HSPB8 in conjunction with cochaperone BAG3, promotes autophagy-mediated removal of misfolded proteins associated with various neurodegenerative diseases. Mutations in HSPB8, previously associated with Charcot Marie Tooth disease type 2L, have recently been linked to an autosomal dominant rimmed vacuolar myopathy (MFM13), and is considered a multisystem proteinopathy. Patients have distal and proximal limb girdle myopathy with muscle biopsy showing fatty replacement, endomysial fibrosis, and rimmed vacuoles leading to muscle atrophy and early demise. We have demonstrated reduced expression of HSPB8, altered autophagy and TDP-43 accumulation in patient fibroblasts. Using CRISPR technology, we generated a knock-in Hspb8 mouse model of the c.515dupC hot spot frameshift variant to study disease pathology. Overexpressed murine Hspb8 frameshift mutant (c.515dupC, fs) displays insolubility and aggregation propensity in Murine Neuroblastoma X Spinal Cord 34 (NSC-34) cells. Mutant Hspb8 mice developed late-onset muscle weakness beginning at 15 months. Muscle biochemical analyses revealed reduced HSPB8 levels, increased TDP-43, and altered autophagy markers, partially recapitulating the human phenotype. Fiber type analysis, neuromuscular junction integrity, and motor neurons show mild myopathy without neurodegeneration. Given the lack of available treatments, we evaluated trehalose, a natural disaccharide that induces HSPB8 and enhances autophagy. Administration of 2% trehalose in drinking water improves motor performance, restores HSPB8 expression, and ameliorates autophagic and TDP-43 pathology in mutant mice. These findings support the value of our preclinical models for translational studies, and autophagy enhancement as a potential therapeutic strategy for HSPB8-related myopathy.

genetics↗

bioRxiv2026

Cumulative Transfer Function for Assessment of MRI-Induced RF Heating Risk in Pediatric Patients Implanted with Bifurcated Leads

PurposeRF-induced heating remains a major barrier to MRI access for patients with epicardial cardiac implantable electronic devices (CIEDs). Although ISO/TS 10974 Tier-3 transfer function (TF) methods are established for unbranched leads, no analogous framework exists for bifurcated leads, in which branch asymmetry and inter-branch coupling may substantially alter heating. We developed and validated a cumulative transfer function (cTF) framework to address this gap. MethodsFollowing ISO/TS 10974 Tier-3 formalism, we measured, calibrated, and validated cTFs for a commercial 35 cm bipolar epicardial lead at 1.5 T. The framework explicitly accounts for branch-specific response and cross-branch coupling. Validation was performed with 24 canonical lead configurations in a homogeneous phantom and, without recalibration, in a heterogeneous anthropomorphic pediatric phantom with clinically derived trajectories. A single-branch TF approximation served as a comparator. The validated cTF was applied to predict RF heating across adult and pediatric human models at multiple imaging landmarks. ResultsCompared with the single-branch TF approximation, the cTF reduced prediction error by nearly 70% in the primary validation dataset. In secondary validation, the cTF maintained low error across clinically relevant trajectories and imaging landmarks. In human models, the framework revealed marked anatomy- and landmark-dependent variation in predicted heating for the tested 35 cm lead, with low predicted heating in pediatric models and substantially higher heating in selected adult chest and upper abdominal imaging scenarios. ConclusionThe cTF provides a validated framework for RF-heating assessment of bifurcated leads and substantially improves prediction accuracy over single-branch TF approximations that neglect branch coupling.

bioengineering↗

bioRxiv2026

Mitochondrial-targeted therapy with elamipretide preserves cardiac function and prevents late mortality in murine sepsis-induced cardiac dysfunction.

Sepsis-induced cardiac dysfunction (SICD) occurs in nearly half of septic patients, is associated with increased mortality, and lacks targeted therapy. Emerging evidence implicates impaired mitochondrial function and metabolic inflexibility as central contributors to myocardial depression. Here, we characterized SICD in a murine model of polymicrobial sepsis and evaluated the therapeutic potential of the cardiolipin-stabilizing peptide elamipretide (Ela). Sepsis induced marked impairments in cardiac performance, accompanied by reductions in cardiac cardiolipin content, impaired mitochondrial respiratory capacity localized to complex I, and altered substrate utilization. Integration of stable isotope metabolic flux tracing with lipidomic, metabolomic, and proteomic analyses identified a convergent metabolic bottleneck at the level of the electron transport system. This defect was associated with upstream accumulation of acetyl-CoA, Co-A esters, and ketone bodies, consistent with impaired oxidative flux and energetic failure. Administration of a single early dose of Ela restored cardiolipin content, complex I function, normalized metabolic flux, improved cardiac function during both acute sepsis and recovery, and completely prevented late sepsis-related mortality. These findings identify cardiolipin-dependent mitochondrial dysfunction as a central pathogenic mechanism underlying SICD and position mitochondrial-targeted therapy as a promising therapeutic strategy in sepsis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/736409v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1ca5b47org.highwire.dtl.DTLVardef@2ecfc2org.highwire.dtl.DTLVardef@149ccb9org.highwire.dtl.DTLVardef@1fbcb6_HPS_FORMAT_FIGEXP M_FIG C_FIG Ela improves SICD by stabilizing cardiolipin species and improving mitochondrial complex I function. SICD depicted in red denotes conditions altered compared to healthy control cardiomyocyte, SICD+Ela depicted in green denotes changes relative to SICD. SICD, sepsis-induced cardiac dysfunction; ELA, elamipretide; ADP, adenosine diphosphate; ATP, adenosine triphosphate; ROS, reactive oxygen species.

physiology↗

bioRxiv2026

Real-Time Assessment of Murine Cardiac Oxygenation Using Photoacoustic Imaging

BackgroundPerioperative incidents such as hypoxic cardiac injury often have subtle or nonspecific clinical manifestations. Reduction in myocardial oxygenation precedes biochemical changes, as well as electrical and functional changes. Photoacoustic imaging (PAI) is a modality that uses laser irradiation of tissue to generate ultrasonic waves, enabling spatially resolved quantitative mapping of oxygenated and deoxygenated haemoglobin. We investigated the utility of PAI for real-time monitoring of myocardial and great vessel oxygenation. MethodsMale CD-1 mice were anaesthetised, and photoacoustic and simultaneous B-mode images were acquired of the myocardium and right ventricular outflow tract (RVOT), the pulmonary artery, and aorta. PAI was performed at fractional inspired oxygen levels (FiO2) of 100%, 21%, and then 10%. Separate cohorts of mice were exposed to increasing intravenous doses of either combined phenylephrine and isoprenaline, or individual administration of vasoactive or adrenergic agents. ResultsPAI reliably distinguished changes in oxygenation in the RVOT cavity, pulmonary artery, aorta, and myocardium. PAI detected hypoxia-induced changes in oxygenation, revealing greater desaturation in the myocardium than in the RVOT (-9.85%, 95% CI -14.94 to -4.77, P<0.0001). Escalating doses of phenylephrine and isoprenaline caused a progressive desaturation of the myocardium and RVOT (mean [95% CI]; myocardium 16 mg/kg: -14.64% [-27.62 to -1.65], P=0.0038 and RVOT 32 mg/kg: -18.71% [-32.15 to -5.27], P=0.0003). Myocardial deoxygenation was detected before changes in systolic function or electrical abnormalities. ConclusionsThis work demonstrates that PAI can reliably monitor cardiac oxygen desaturation, potentially offering an earlier warning of cardiac dysfunction and injury compared to existing monitoring tools.

physiology↗

bioRxiv2026

Maternal iron deficiency remodels cardiac mitochondria and alters stress responses in hypertensive pregnancy

Maternal iron deficiency (ID) during pregnancy is associated with cardiovascular adaptations, including reduced blood pressure and improved cardiac efficiency in hypertensive pregnancy. However, whether these apparent functional gains are accompanied by preserved cardiac mitochondrial function remains unclear. Given the high metabolic demands of the maternal heart and irons central role in oxidative metabolism, we examined how maternal ID affects cardiac mitochondrial ultrastructure, respiration, dynamics, and redox status in pregnant spontaneously hypertensive rats (SHR) and normotensive Wistar-Kyoto (WKY) rats. Female SHR and WKY rats were fed iron-replete or iron-restricted diets before and throughout gestation. On gestational day 21, cardiac mitochondrial ultrastructure was assessed by transmission electron microscopy, respiration by high-resolution respirometry, mitochondrial dynamics and quality control proteins by immunoblotting, and antioxidant gene expression by RT-qPCR. Iron restriction reduced maternal hemoglobin levels in both strains. ID dams exhibited enlarged, morphologically heterogeneous mitochondria with reduced cristae density and lower succinate-supported respiration. SHR dams exhibited reduced fusion signalling, reflected by a lower L-OPA1:S-OPA1 ratio, lower MFN2 abundance, and further ID-associated reductions in MFN1 and MFN2. In contrast, DRP1 phosphorylation increased in ID-WKY dams. Iron restriction increased LC3-II:I ratio and BNIP3 in SHR, increased PINK1 in both strains, and increased antioxidant gene expression in ID-SHR but decreased in ID-WKY dams. Despite these alterations, downstream apoptosis activation was not observed. Maternal ID was associated with remodelling of myocardial mitochondrial ultrastructure and selectively constrains iron-dependent respiration in hypertensive pregnancy, suggesting favourable hemodynamic adaptations may coexist with underlying bioenergetic constraints in the maternal heart.

physiology↗

bioRxiv2026

A multiomic lifespan signature in genetically diverse, diet-restricted mice

Dietary restriction extends lifespan across model organisms, but the plasma molecular changes mediating this effect remain incompletely characterized. We present a longitudinal multiomic analysis of 2,234 plasma samples from 960 Diversity Outbred mice subjected to intermittent fasting or caloric restriction and followed to natural death. Using mass spectrometry, we quantified 1,512 metabolites, lipids, and proteins and mapped their associations with diet, age and longevity. DR-induced molecular changes scale with caloric intake and modulate inflammatory, lipid catabolism, and oxidative stress pathways. Aging showed a biphasic signature with sharp acceleration beyond 85% of lifespan, demarcating terminal decline. Mediation and survival modeling both identified superoxide dismutase (SODE) and vascular cell adhesion molecule (VCAM1) as top lifespan predictors. Genetic analysis revealed 9,599 QTL, nine of which coincided with previously identified lifespan QTLs, and were largely related to immune regulation. These findings provide a rich multiomic and genetic resource for the aging research community.

systems biology↗

bioRxiv2025

Homology-Based Enzymatic Assembly of Modular T7 Phage Genome

Bacteriophages, viruses that infect bacteria, are pivotal in therapeutic, industrial, and bio-detection applications due to their unique ability to inject DNA into bacterial hosts and change the genetics and behavior of whole bacterial populations. Genetic engineering of phage genomes has expanded their potential applications with several established methods such as Golden Gate assembly, yeast cloning, {lambda} Red recombineering, and CRISPR-Cas systems. Here, we present a novel, efficient method to design and make synthetic bacteriophages in vitro without using restriction enzymes to allow for modular insertion of DNA fragments into the phage genome. The ability to create synthetic bacteriophages in vitro without the use of restriction enzymes allows for simpler engineering without the hassle or cloning limitations encountered when building domesticated bacteriophage genomes.

bioengineering↗

bioRxiv2024

Synthesis and Evaluation of Carmofur Analogs as Antiproliferative Agents, Inhibitors to the Main Protease (Mpro) of SARS-CoV-2, and Membrane Rupture-Inducing Agents

Initially developed as a derivatized analog of 5-fluorouracil for the treatment of colorectal cancer, carmofur has more recently demonstrated potent covalent inhibition of the main protease (Mpro) of SARS-CoV-2. Harnessing our previously described workflow for the optimized preparation of carmofur using benchtop 19F NMR spectroscopy, here, we prepared and evaluated a synthetic library of nine carmofur analogs with a selection of side chain motifs or single-atom substitution to explore the diversifiability of these compounds as Mpro inhibitors, where we discovered that a hexyl carbamate analog outperformed carmofur, and as antiproliferative agents in model human cell lines to identify differences in potency when the carbonyl electrophilicity and/or alkyl side chains are modified. Finally, we describe a novel workflow for the evaluation of membrane-rupturing small molecules through imaging of fluorescently labeled giant unilamellar vesicles (GUVs), and through this, we identified two lipophilic urethane analogs of carmofur bearing dodecyl urethane and octadecyl urethane side chains that have potent membrane-rupturing capability in the nanomolar range, providing insight into a potential mechanism for the in vitro activities of lipidated 5-fluorouracil analogs.

biochemistry↗

bioRxiv2022

Artifacts can be deceiving: The actual location of deep brain stimulation electrodes differs from the artifact seen on magnetic resonance images

IntroductionDeep brain stimulation (DBS) is a common treatment for a variety of neurological and psychiatric disorders. Recent studies have highlighted the role of neuroimaging in localizing the position of electrode contacts relative to target brain areas in order to optimize DBS programming. Among different imaging methods, postoperative magnetic resonance imaging (MRI) has been widely used for DBS electrode localization; however, the geometrical distortion induced by the lead limits its accuracy. In this work, we investigated to what degree the difference between the actual location of the leads tip and the location of the tip estimated from the MRI artifact varies depending on the MRI sequence parameters such as acquisition plane and phase encoding direction, as well as the leads extracranial configuration. Accordingly, an imaging technique to increase the accuracy of lead localization was devised and discussed. MethodsWe designed and constructed an anthropomorphic phantom with an implanted DBS system following 18 clinically relevant configurations. The phantom was scanned at a Siemens 1.5 Tesla Aera scanner using a T1MPRAGE sequence optimized for clinical use and a T1TSE sequence optimized for research purposes. We varied slice acquisition plane and phase encoding direction and calculated the distance between the caudal tip of the DBS lead MRI artifact and the actual tip of the lead, as estimated from MRI reference markers. ResultsImaging parameters and lead configuration substantially altered the difference in the depth of the lead within its MRI artifact on the scale of several millimeters - with a difference as large as 4.99 millimeters. The actual tip of the DBS lead was found to be consistently more rostral than the tip estimated from the MR image artifact. The smallest difference between the tip of the DBS lead and the tip of the MRI artifact using the clinically relevant sequence (i.e., T1MPRAGE) was found with the sagittal acquisition plane and anterior-posterior phase encoding direction. Discussion/ConclusionThe actual tip of an implanted DBS lead is located up to several millimeters rostral to the tip of the leads artifact on postoperative MR images. This distance depends on the MRI sequence parameters and the DBS systems extracranial trajectory. MRI parameters may be altered to improve this localization.

neuroscience↗

bioRxiv2020

Identification of novel HPFH-like mutations by CRISPR base editing that elevates the expression of fetal hemoglobin

Switching hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin is an effective strategy for the treatment of beta-hemoglobinopathies. Fetal hemoglobin expression is down-regulated in the postnatal period due to the interplay of transcription regulators with the HBG promoters. However, in the hereditary persistence of fetal hemoglobin (HPFH) condition, naturally occurring point mutations in the HBG promoter causes continued expression of fetal globin even during adulthood. Inspired by this natural phenomenon, we screened the proximal promoter of human HBG genes using adenine and cytosine base editors to identify other nucleotide substitutions that could potentially lead to elevated levels of fetal globin. Both the base editors efficiently and precisely edited at the target sites with a minimal generation of indels and no deletion of one of the duplicated HBG genes. Through systematic tiling across the HBG proximal promoter, we identified multiple novel target sites that resulted in a significant increase in fetal globin levels. Further, we individually validated the top eight potential target sites from both the base editors and observed robust elevation in the fetal globin levels up to 47 %, without any detrimental effects on erythroid differentiation. Our screening strategy resulted in the identification of multiple novel point mutations and also validated the known non-deletional HPFH mutations that could elevate the fetal globin expression at therapeutically relevant levels. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter that normally mediates fetal globin silencing and identify additional targets for therapeutic upregulation of fetal hemoglobin.

genomics↗

bioRxiv2020

The effect of device configuration and patient body composition on image artifact and RF heating of deep brain stimulation devices during MRI at 1.5T and 3T

BACKGROUNDPatients with deep brain stimulation (DBS) implants have limited access to MRI due to safety concerns associated with RF-induced heating. Currently, MRI in these patients is allowed only in 1.5T horizontal scanners and with pulse sequences with reduced power. Nevertheless, off-label use of MRI at 3T is increasingly reported based on limited safety assessments. Here we present results of systematic RF heating measurements for two commercially available DBS systems during MRI at 1.5T and 3T. PURPOSETo assess the effect of imaging landmark, DBS lead configuration, and patient body composition on RF heating of DBS leads during MRI at 1.5 T and 3T. STUDY TYPEPhantom study. POPULATION/SUBJECTS/PHANTOM/SPECIMEN/ANIMAL MODELGel phantoms and cadaver brain. FIELD STRENGTH/SEQUENCE1.5T and 3T, T1-weighted turbo spin echo. ASSESSMENTRF heating was measured at tips of DBS leads implanted in brain-mimicking gel. STATISTICAL TESTSNone. RESULTSWe observed substantial fluctuation in RF heating mainly affected by phantom composition and DBS lead configuration, ranging from 0.14{degrees}C to 23.73{degrees}C at 1.5 T, and from 0.10{degrees}C to 7.39{degrees}C at 3T. The presence of subcutaneous fat substantially altered RF heating at electrode tips (-3.06{degrees}C < {Delta}T < 19.05{degrees}C). Introducing concentric loops in the extracranial portion of the lead at the surgical burr hole reduced RF heating by up to 89% at 1.5T and up to 98% at 3T compared to worst case heating scenarios. DATA CONCLUSIONDevice configuration and patient body composition significantly altered the RF heating of DBS leads during MRI at 1.5T and 3T. Interestingly, certain lead trajectories consistently reduced RF heating and image artifact over different imaging landmarks, RF frequencies, and phantom compositions. Such trajectories could be implemented in patients with minimal disruption to the surgical workflow.

bioengineering↗

bioRxiv2020

Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts

The decoy exon model has been proposed to regulate a subset of intron retention (IR) events involving predominantly larger introns (>1kb). Splicing reporter studies have shown that decoy splice sites are essential for activity, suggesting that decoys act by engaging intron-terminal splice sites and competing with cross-intron interactions required for intron excision. The decoy model predicts that antisense oligonucleotides blocking decoy splice sites in endogenous pre-mRNA should increase productive gene expression by reducing IR. Indeed, we now demonstrate that targeting a decoy 5' splice site in the O-GlcNAc transferase (OGT) gene reduced IR from [~]80% to [~]20% in primary human erythroblasts, accompanied by increases in spliced OGT RNA and OGT protein expression. The remaining OGT IR was refractory to antisense treatment and might be mediated by independent mechanism(s). In contrast, other retained introns were strongly dependent on decoy function, since IR was nearly eliminated by antisense targeting of 5' splice sites. Genes in the latter group encode the widely expressed splicing factor (SF3B1), and the erythroid-specific structural protein, alpha-spectrin (SPTA1). These results show that modulating decoy exon function can dramatically alter IR, and suggest that dynamic regulation of decoy exons could be a mechanism to fine tune gene expression post-transcriptionally in many cell types.

molecular biology↗

bioRxiv2018

CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells.

Sickle Cell Disease and {beta}-thalassemia, which are caused by defective or deficient adult {beta}-globin (HBB) respectively, are the most common serious genetic blood diseases in the world. Expression of the fetal {beta}-like globin, also known as {gamma}-globin, can ameliorate both disorders by serving in place of the adult {beta}-globin. Here we use CRISPR-Cas9 gene editing to explore a putative {gamma}-globin silencer region identified by comparison of naturally-occurring deletion mutations associated with up-regulated {gamma}-globin. We find that deletion of a 1.7 kb consensus element or select 350 bp sub-regions from bulk populations of cells increases levels of fetal hemoglobin (HbF) or {gamma}-globin. Screening of individual sgRNAs in one sub-region revealed three single guides that caused mild increases in {gamma}-globin expression. However, clonal cell lines with the 1.7 kb region deleted did not up-regulate {gamma}-globin and neither did lines with either of two of sub-regions identified in the screen deleted. These data suggest that the region is not an autonomous {gamma}-globin silencer, and thus by itself is not a suitable therapeutic target in the {beta}-hemoglobinopathies.

genetics↗

bioRxiv2018

Controlled cycling and quiescence enables homology directed repair in engraftment-enriched adult hematopoietic stem and progenitor cells

Hematopoietic stem cells (HSCs) are the source of all blood components, and genetic defects in these cells are causative of disorders ranging from severe combined immunodeficiency to sickle cell disease. However, genome editing of long-term repopulating HSCs to correct mutated alleles has been challenging. HSCs have the ability to either be quiescent or cycle, with the former linked to stemness and the latter involved in differentiation. Here we investigate the link between cell cycle status and genome editing outcomes at the causative codon for sickle cell disease in adult human CD34+ hematopoietic stem and progenitor cells (HSPCs). We show that quiescent HSPCs that are immunophenotypically enriched for engrafting stem cells predominantly repair Cas9-induced double strand breaks (DSBs) through an error-prone non-homologous end-joining (NHEJ) pathway and exhibit almost no homology directed repair (HDR). By contrast, non-quiescent cycling stem-enriched cells repair Cas9 DSBs through both error-prone NHEJ and fidelitous HDR. Pre-treating bulk CD34+ HSPCs with a combination of mTOR and GSK-3 inhibitors to induce quiescence results in complete loss of HDR in all cell subtypes. We used these compounds, which were initially developed to maintain HSCs in culture, to create a new strategy for editing adult human HSCs. CD34+ HSPCs are edited, allowed to briefly cycle to accumulate HDR alleles, and then placed back in quiescence to maintain stemness, resulting in 6-fold increase in HDR/NHEJ ratio in quiescent, stem-enriched cells. Our results reveal the fundamental tension between quiescence and editing in human HSPCs and suggests strategies to manipulate HSCs during therapeutic genome editing.

cell biology↗

bioRxiv2017

Desert Tortoises in the Genomic Age: Population Genetics and the Landscape

The California Department of Fish and Wildlife (CDFW) provided research funds to study the conservation genomics and landscape genomics of the Mojave desert tortoise, Gopherus agassizii, in response to the Desert Renewable Energy Conservation Plan (DRECP). To do this, we consolidated tissue samples of the desert tortoise from across the species range within California and southern Nevada, generated a DNA dataset consisting of full genomes of 270 tortoises, and analyzed the way in which the environment of the desert tortoise has determined modern patterns of relatedness and genetic diversity across the landscape. Here we present the implications of these results for the conservation and landscape genomics of the desert tortoise. Our work strongly indicates that several well-defined genetic groups exist within the species, including a primary north-south genetic discontinuity at the Ivanpah Valley and another separating western from eastern Mojave samples. We also use existing desert tortoise habitat modeling data with a novel extension of genetic \"resistance distance\" using geographic maps of continuous space to predict the relative impacts of five proposed development alternatives within the DRECP and rank them with respect to their likely impacts on desert tortoise gene flow and connectivity in the Mojave. Finally, we analyzed the impacts of each of the 214 distinct proposed development area \"chunks,\" derived from the proposed development polygons, and ranked each chunk in terms of its range-wide impacts on desert tortoise gene flow.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC=\"FIGDIR/small/195743_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (147K):\norg.highwire.dtl.DTLVardef@b60416org.highwire.dtl.DTLVardef@1c649f2org.highwire.dtl.DTLVardef@120e625org.highwire.dtl.DTLVardef@e59b34_HPS_FORMAT_FIGEXP M_FIG C_FIG PrefaceO_ST_ABSContextC_ST_ABSThe following document is a report that was submitted to the California Department of Fish and Wildlife, describing a series of analyses to help understand the impacts of several alternative spatial configurations of renewable energy development on gene flow of the federally threatened Mojave desert tortoise. These development alternatives were the centerpiece of the Desert Renewable Energy Conservation Plan (DRECP), a landscape-level land use planning initiative undertaken by the Bureau of Land Management (BLM), U.S. Fish and Wildlife Service (USFWS), California Energy Commission (CEC), and the California Department of Fish and Wildlife (CDFW). We were tasked by the California Department of Fish and Wildlife with providing a detailed analysis of these alternative plans on desert tortoise gene flow, and submitted the report for the public comment period for the initial implementation of the DRECP.\n\nFuture PlansO_ST_ABSCurrent state of landscape-level planning for the Mojave desert tortoiseC_ST_ABSThe five proposed land use configuration alternatives analyzed in the subsequent report include public and private lands spread across several counties in California. Shortly after the end of the DRECPs public comment period, the government agencies that developed the DRECP announced that they would be splitting its implementation into two phases: one that deals with land use decisions on BLM-controlled lands and one that deals with non-BLM areas (Sahagun 2015).\n\nPhase I of the DRECP was approved by the Bureau of Land Management on September 14, 2016 (U.S. Bureau of Land Management 2016). This phase includes land use planning decisions for BLM-administered lands. Specifically, 388,000 acres of public lands were designated as development focus areas (DFAs). In applications for leasing lands for renewable energy development, DFAs will not require the same degree of environmental evaluation prior to permitting, as theyve already been evaluated in the context of the DRECP. The application process for renewable energy development within DFAs will be streamlined to encourage development in these areas. Phase I also designated a total of 6,527,000 acres for natural resource conservation. This includes California Desert National Conservation Lands, Areas of Critical Environmental Concern, and Wildlife Allocations. A further 2,691,000 acres were designated for recreation under Phase I. Phase II of the DRECP is currently under development in conjunction with county-level governments to extend this landscape-level planning beyond BLM-administered lands.\n\nAuthor ContributionsThis was a collaborative report. Evan McCartney-Melstad performed the simulations of the low-coverage full genome approach (see Figure 2); conducted all of the laboratory work to generate the genome sequences; performed all of the bioinformatic analyses to bring the raw sequence data to the various stages required for different analyses; wrote the software to quickly estimate pairwise genetic relationships between individuals using read count data in low coverage sequence data (www.github.com/atcg/cPWP); performed some of the population genetic analyses; and wrote and edited several sections of the report.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/195743_fig2.gif\" ALT=\"Figure 2\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@30a49forg.highwire.dtl.DTLVardef@187c3d8org.highwire.dtl.DTLVardef@4abe98org.highwire.dtl.DTLVardef@126febe_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Comparison of two different sequencing approaches in their ability to differentiate very slightly differentiated populations (Fst=0.001)\n\nC_FIG Peter Ralph (in collaboration with Gideon Bradburd and Erik Lundgren) invented and implemented the random walk-based gene flow model that we used to estimate reductions in gene flow due to development, and also developed the theory behind the read-based pairwise pi and genetic covariance estimation used here, in addition to writing and editing several sections of the report. Gideon Bradburd also performed some of the population genetic analyses and wrote and edited several sections of the report. Jannet Vu collected and curated the spatial environmental data and generated the maps that are included in the report (Figures 10, A10-A13), and also wrote Appendices I and IV. Bridgette Hagerty, Fran Sandmeier, Chava Weitzman, and C. Richard Tracy contributed approximately 1,000 desert tortoise blood samples that they collected (at great effort), in addition to knowledge of tortoise ecology and conservation, as well as the results of previous microsatellite-based genetic analyses and editing of the report. H. Bradley Shaffer wrote and edited several sections of the report, and is listed as the lead author for his role in conceiving of and obtaining funding support for the project.\n\nO_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC=\"FIGDIR/small/195743_fig10.gif\" ALT=\"Figure 10\">\nView larger version (82K):\norg.highwire.dtl.DTLVardef@11e99acorg.highwire.dtl.DTLVardef@1faf2f5org.highwire.dtl.DTLVardef@64c440org.highwire.dtl.DTLVardef@1907837_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 10.C_FLOATNO Spatial configuration of the proposed development chunks (see Appendix 4).\n\nC_FIG

evolutionary biology↗