Search

PDF file - 775K

PDF file - 61K

Supplementary Figure 2 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

Supplementary Figure 5 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

Supplementary Figure 7 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

Supplementary Figure 4 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

Supplementary Figure 8 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

PDF file - 476K

PDF file - 453K

PDF file - 274K

The Myc/Max/Mad family of transcription factors and the eukaryotic initiation factor 4F (eIF4F) complex play fundamental roles in regulating cell growth, proliferation, differentiation, and oncogenic transformation. eIF4F is involved in the recruitment of ribosomes to mRNAs and is thought to generally be the rate-limiting phase of translation. Here, we show that c-Myc directly activates transcription of the three subunits of eIF4F (eIF4E, eIF4AI, and eIF4GI). These transcriptional effects are mediated through canonical E-boxes (5′CACGTG3′) present in the promoters of these genes. In addition, the c-Myc antagonist Mad1 down-regulates the expression of eIF4F subunits. We also show that MycER activation stimulates protein synthesis at the level of translation initiation. Increased eIF4F levels result in stimulation of c-Myc mRNA translation specifically, as assessed by quantitative reverse transcription–PCR. We use a murine model of lymphomagenesis to show the expression of eIF4F subunits is also up-regulated by c-Myc in vivo. Our results suggest the presence of a feedforward loop involving c-Myc and eIF4F that serves to link transcription and translation and that could contribute to the effects of c-Myc on cell proliferation and neoplastic growth. [Cancer Res 2008;68(13):5326–34]

PDF file - 98K

Supplementary Figure 3 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

PDF file - 247K

PDF file - 662K

Supplementary Methods, Figure Legends 1-8 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

PDF file - 280K

Supplementary Figure 1 from c-Myc and eIF4F Are Components of a Feedforward Loop that Links Transcription and Translation

PDF file - 309K

To determine the frequency of detection and the age and sex associations of autoimmune/paraneoplastic encephalitis antibody biomarkers (AE-Abs).There were 42,032 patients tested in the Mayo Clinic Neuroimmunology Laboratory between January 2018 and December 2019 for AE-Abs in serum or cerebrospinal fluid (CSF), including NMDA-R-IgG, AMPA-R-IgG, GABAAdult serum analysis (22,472 patients; 56% female) revealed that 814 (3.6%) were positive: NMDA-R-IgG (24.6%)GAD65-IgG (21.5%)LGI1-IgG (20.5%)others. Of children (5649; 50% female), 251 (4.4%) were positive: NMDA-R-IgG (53.1%)MOG-IgG1 (32%)GAD65-IgG (7.1%)others. Adult CSF analysis (18,745 patients; 54% female) revealed that 796 (4.2%) were positive: NMDA-R-IgG (39.7%)GAD65-IgG (28.5%)LGI1-IgG (11.4%)others. Of children (5136; 50% female), 282 (5.5%) were positive: NMDA-R-IgG (88.1%)GAD65-IgG (8.7%)others. Age younger than 20 years was associated with NMDA-R-IgG and MOG-IgG1 (odds ratio [OR], 8.11 and 7.84, respectively; P.001). Age older than 65 years was associated with GABAThe most frequent AE-Abs detected were NMDA-R-IgG, GAD65-IgG, LGI1-IgG, and MOG-IgG1. Age and sex associations may suggest paraneoplastic, or aging influences on neurologic autoimmunity.

To verify the analytical performance of a new mass spectrometry-based method, termed MASS-FIX, when screening for plasma cell disorders in a routine clinical laboratory.Results from 19,523 unique patients tested for an M-protein between July 24, 2018, and March 6, 2020, by a combination serum protein electrophoresis (SPEP) and MASS-FIX were examined for consistency with pretest implementation performance. MASS-FIX's ability to verify abnormal results from SPEP and free light chain measurements was then compared with that of immunofixation electrophoresis (IFE) using a separate cohort of 52,586 patients tested by SPEP/IFE during the same period.Overall, 62.4% of our cohort was negative for an M-protein. Importantly, 7.3% of all specimens had an M spike on SPEP (0.1 to 8.5 g/dL) and MASS-FIX detected an M-protein in all these samples. Of all samples, 30.3% had M-proteins that were detected by MASS-FIX but the SPEP finding was too small for quantification. Of the positive samples, 5.7% contained a therapeutic monoclonal antibody. Of the positive samples, 4.1% had an N-glycosylated light chain (biomarker of high-risk plasma cell disorders). MASS-FIX confirmed a higher percentage of SPEP abnormalities than IFE. MASS-FIX was slightly more sensitive than IFE when confirming an M-protein in samples with an abnormal free light chain ratio. MASS-FIX had a very low sample repeat rate (1.5%). MASS-FIX was highly automatable resulting in a higher number of samples/technologist/day than IFE (∼30% more).Overall, MASS-FIX was successful in maintaining validation characteristics. MASS-FIX was more sensitive in confirming SPEP abnormalities when compared with IFE. Ability to detect therapeutic monoclonal antibodies and glycosylated light chains was distinctly advantageous.

This study was undertaken to report clinical presentations and outcomes of CASPR2-IgG-associated seizures.Mayo Clinic Neuroimmunology database was queried to identify CASPR2-IgG-seropositive (CASPR2-IgG+) patients evaluated at our institution (2009-2019).Of the 53 CASPR2-IgG+ patients (titer ≥ 1:10), 20 had seizures (38%). All seizure patients were male, with median onset age of 68 years. Eighteen (90%) had seizures at initial presentation. One patient was found to have malignancy (colon adenocarcinoma). Two patients had coexisting LGI1-IgG. Twelve patients had archived sera, which on titration had CASPR2-IgG titers ≥ 1:100. Fifteen patients (75%) met criteria for autoimmune encephalitis. Patients most commonly presented with focal onset, nonmotor seizures with impaired awareness (n = 14, 70%). Eleven patients also had focal motor and/or sensory seizures as one of the seizure semiologies. The majority of patients (n = 11, 55%) developed generalized tonic-clonic seizures during their disease course. Seizure clusters occurred in 12 patients. In addition to seizures, patients developed cognitive disturbance (n = 16, 80%), episodic emotional lability (n = 13, 65%), paroxysmal dizziness (n = 9, 45%), episodic ataxia (n = 6, 30%), and chronic ataxia (n = 9, 45%). Only three patients (15%) had coexisting peripheral nervous system involvement. Frontotemporal or temporal ictal and/or interictal electroencephalographic abnormalities were present among nine patients, and three had multifocal epileptiform abnormalities. Eight patients (40%) had medial temporal T2/fluid-attenuated inversion recovery hyperintensity on brain magnetic resonance imaging. Elevated cerebrospinal fluid protein and/or lymphocytic pleocytosis was present in most cases (13/14, 93%). Thirteen patients reached seizure freedom following initiation of antiseizure medication (ASM; n = 4) or a combination of immunotherapy and ASM (n = 9). Median duration of follow-up was 25 months (range = 2-136 months).CASPR2-IgG evaluation should be considered among older male patients with new onset focal seizures and impaired awareness often occurring in clusters with/without features of encephalitis. Coexisting neurological manifestations, including episodic emotional lability, ataxia, and paroxysmal dizziness, also aid in the diagnosis.

ObjectivesTo report the expanded neurological presentations and oncological associations of tripartite motif-containing protein 46 (TRIM46)-IgG seropositive patients.MethodsArchived sera/cerebrospinal fluid (CSF) were evaluated by tissue-based immunofluorescence assay to identify patients with identical axon initial segment (AIS)-specific staining pattern. Phage immunoprecipitation sequencing (PhIP-Seq) was used to identify the putative autoantigen.ResultsIgG in serum (17) and/or CSF (16) from 25 patients yielded unique AIS-specific staining on murine central nervous system (CNS) tissue. An autoantibody specific for TRIM46 was identified by PhIP-Seq, and autoantigen specificity was confirmed by transfected COS7 cell-based assay. Clinical information was available for 22 TRIM46-IgG seropositive patients. Fifteen were female (68%). Median age was 67 years (range 25–87). Fifteen (68%) patients presented with subacute cerebellar syndrome (six isolated; nine with CNS accompaniments: encephalopathy (three), brainstem signs (two), myelopathy (two), parkinsonism (one)). Other phenotypes included limbic encephalitis (three), encephalopathy with/without seizures (two), myelopathy (two). Eighteen (82%) had cancer: neuroendocrine carcinomas (9; pancreatic (3), small-cell lung (4), oesophagus (1), endometrium (1)), adenocarcinomas (6; lung (2), ovarian (2), endometrial (1), breast (1)), sarcoma (2) and gastrointestinal tumour (1). Neurological symptoms in three followed immune checkpoint inhibitor (ICI) administration.ConclusionsThis study supports TRIM46-IgG being a biomarker of paraneoplastic CNS disorders and expands the neurological phenotypes, oncological and ICI-related adverse event associations.

Immune-mediated necrotizing myopathy (IMNM) is considered a rare subtype of the immune-mediated myopathies, but its incidence and prevalence are unknown. In this study we aimed to determine the incidence and prevalence of IMNM among adults in Olmsted County, Minnesota.We identified adult patients with IMNM, as defined by the 2016 European Neuromuscular Centre diagnostic criteria, among residents of Olmsted County, Minnesota over a 20-year period.Seven patients fulfilled the inclusion criteria. Six patients were tested for IMNM antibodies: four were anti-3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) positive, one was anti-signal recognition particle positive, and one was seronegative. The incidence of IMNM during 2010-2019 was 8.3 per million person-years. The prevalence of IMNM in 2010 was 1.85 per 100 000 people at least 50 years of age. Median age at symptom onset was 64 (range, 52-86) years and median time from symptom onset to diagnosis was 3 (range,1 to 156) months. Statin use among anti-HMGCR IMNM patients, but not the entire IMNM cohort, was higher than in controls (P = .024). Two IMNM patients developed cancers. The incidence of malignancy in IMNM was not higher than that of the general population. Treatment outcome was favorable in all patients except for one patient with delayed treatment and another with insufficient therapy. Among three deceased patients, one died of cancer and another died of IMNM-related cardiorespiratory complications.IMNM is a rare disease. Its prevalence is one tenth that of inclusion-body myositis in Olmsted County, Minnesota. IMNM patients in our cohort were not at higher risk for developing cancer.

Objectives To investigate immune-mediated necrotizing myopathy (IMNM) association with cancer and its clinical implications. Methods IMNM cases were identified 1 January 2000 to 31 December 2020 matching sex and age controls (4:1). Results A total of 152 patients with IMNM were identified and among serologically tested, 60% (83/140) were HMGCR-IgG+, 14% (20/140) were SRP-IgG+ and 26% (37/140) were seronegative. Cancer rates were not significantly different between serological subgroups; 18.1% (15/83) HMGCR-IgG+, 25% (5/20) SRP-IgG+ and 30% (11/37) seronegative (P = 0.34). Cancer screening was performed within 12 months from IMNM diagnosis in 88% (134/152) (whole-body CT plus FDG-PET CT in 53, CT alone in 72 and FDG-PET alone in 9). FDG-PET/CT was positive in 73% (25/34) of cancers. Increasing age was the only risk associated with cancer (P = 0.02). The odds of developing cancer at ±3 or ±5 years from IMNM diagnosis was not higher than controls (OR = 0.49; CI: 0.325–0.76). Lifetime IMNM diagnosis of cancer was less compared with controls (OR = 0.5 CI: 0.33–0.78, P = 0.002). Most patients responded to treatment (137/147, P Conclusions Greater cancer risk is not observed in IMNM vs controls. Cancer screening in IMNM should be individualized based on age-personal and family history, including consideration of FDG-PET/CT. Immune-treatment response did not differ with cancer.

Longitudinal studies assessing durability of the anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) humoral immune response have generated conflicting results. This has been proposed to be due to differences in patient populations, the lack of standardized methodologies, and the use of assays that measure distinct aspects of the humoral response. SARS-CoV-2 antibodies were serially measured in sera from a cohort of 44 well-characterized convalescent plasma donors over 120 days post-COVID-19 symptom onset, utilizing eight assays, which varied according to antigen source, the detected antibody isotype, and the activity measured (i.e., binding, blocking, or neutralizing). While the majority of assays demonstrated a gradual decline in antibody titers over the course of 120 days, the two electrochemiluminescence immunoassay Roche assays (Roche Diagnostics Elecsys anti-SARS-CoV-2 [qualitative, nucleocapsid based] and Roche Diagnostics Elecsys anti-SARS-CoV-2 S [semiquantitative, spike based]), which utilize dual-antigen binding for antibody detection, demonstrated stable and/or increasing antibody titers over the study period. This study is among the first to assess longitudinal, rather than cross-sectional, SARS-CoV-2 antibody profiles among convalescent COVID-19 patients, primarily using commercially available serologic assays with Food and Drug Administration emergency use authorization. We show that SARS-CoV-2 antibody detection is dependent on the serologic method used, which has implications for future assay utilization and clinical value.

Type 1 diabetes mellitus (T1DM) can occur at any age, the presence of diabetes related autoantibodies predicts increased risk of disease and supports an autoimmune etiology for T1DM. Since 2017, Mayo Clinic Laboratories has been offering a comprehensive type 1 diabetes autoantibody evaluation (DM1Eval) which includes testing for 4 autoantibodies targeting glutamic acid decarboxylase autoantibodies (GAD), protein tyrosine phosphatase-like islet antigen 2 (IA-2), insulin (IAA), and zinc transporter 8 protein (ZnT8). The aim of this study was to determine the frequency of individual antibodies and antibody clusters (2, 3 or 4) stratified into 4 ages groups (children 0-17, young adult 18-35, middle aged 36-55 and older >55 years). Over a 30 month period (June 2017-Nov 2019) the DM1Eval was performed on 6,446 samples. At least 1 autoantibody was found in 3596 (56%) of all samples: 68% of children, 49% of young adults, 40% of middle aged and 41% of older adults. In patients with at least 1 antibody positive, GAD 65 antibodies were the most common in all age groups followed by ZnT8 in those Autoantibody clusters of 3 or 4 antibodies were more frequently encountered in younger patients (41% of pediatric and 27% of young adult patients in contrast to just 12% in middle and older age groups). Disclosure A.R. Dahl: None. S. Pittock: None. A. McKeon: None. J. Foster: None. J. Mills: None.

SUMMARY Targeting translation initiation is an emerging anti-neoplastic strategy that capitalizes on de-regulated upstream MAPK and PI3K-mTOR signaling pathways in cancers. A key regulator of translation that controls ribosome recruitment flux is eukaryotic initiation factor (eIF) 4F, a hetero-trimeric complex composed of the cap binding protein eIF4E, the scaffolding protein eIF4G, and the RNA helicase eIF4A. Small molecule inhibitors targeting eIF4F display promising anti-neoplastic activity in preclinical settings. Among these are some rocaglate family members that are well tolerated in vivo, deplete eIF4F of its eIF4A helicase subunit, have shown activity as single agents in several xenograft models, and can reverse acquired resistance to MAPK and PI3K-mTOR targeted therapies. Herein, we highlight the power of using genetic complementation approaches and CRISPR/Cas9-mediated editing for drug-target validation ex vivo and in vivo, linking the anti-tumor properties of rocaglates to eIF4A inhibition., Graphical abstract

Research has shown there is a positive relationship between urban greenness and the well-being of city residents. But greenness is often unevenly distributed across a city, raising environmental justice issues. In 2011 and 2012 the USDA Forest Service, Forest Inventory and Analysis program installed ground plots in the urbanized areas of Oregon and Washington. We analyze these data for the urban areas west of the Cascade Mountains, linking it with demographic data from the U.S. Census to examine the relationship between greenness and socioeconomic status at a sub-regional scale. To explore some relations between urban forest measures and socioeconomic conditions and measures we developed four models: presence of tree canopy cover with a logistic mixed model, and on a subset of the data, percent tree canopy cover with a linear mixed model and tree count and tree species count with Poisson mixed models. We found that median household income, house value, land use, and years in the Tree City USA program contributed to explaining measures of greenness, such as canopy cover presence, percent canopy cover, tree counts, and tree species counts. This agrees with other studies, but does so at a broad scale covering the most densely populated areas in the Pacific Northwest.

PTP1B and TC-PTP are highly related protein-tyrosine phosphatases (PTPs) that regulate the JAK/STAT signaling cascade essential for cytokine-receptor activation in immune cells. Here, we describe a novel immunotherapy approach whereby monocyte-derived dendritic cell (moDC) function is enhanced by modulating the enzymatic activities of PTP1B and TC-PTP. To downregulate or delete the activity/expression of these PTPs, we generated mice with PTP-specific deletions in the dendritic cell compartment or used PTP1B and TC-PTP specific inhibitor. While total ablation of PTP1B or TC-PTP expression leads to tolerogenic DCs via STAT3 hyperactivation, downregulation of either phosphatase remarkably shifts the balance toward an immunogenic DC phenotype due to hyperactivation of STAT4, STAT1 and Src kinase. The resulting increase in IL-12 and IFNγ production subsequently amplifies the IL-12/STAT4/IFNγ/STAT1/IL-12 positive autocrine loop and enhances the therapeutic potential of mature moDCs in tumor-bearing mice. Furthermore, pharmacological inhibition of both PTPs improves the maturation of defective moDCs derived from pancreatic cancer (PaC) patients. Our study provides a new advance in the use of DC-based cancer immunotherapy that is complementary to current cancer therapeutics.

The detection and quantification of monoclonal-proteins (M-proteins) are necessary for the diagnosis and evaluation of response in plasma cell dyscrasias. Immunoglobulin enrichment-coupled with matrix-assisted laser desorption ionization time-of-flight mass-spectrometry (MASS-FIX) is a simple and inexpensive method to identify M-proteins, but its clinical generalizability has not yet been elucidated. We compared MASS-FIX to protein electrophoresis (PEL), serum/urine immunofixation-electrophoresis (IFE), and quantitative serum free-light chain (FLC) for the identification of M-proteins in different clinical diagnoses. Paired serum and urine samples from 257 patients were tested. There were six patients for whom s-IFE and FLC ratio were positive and serum MASS-FIX was negative, but when serum and urine MASS-FIX results were combined, only one patient with light chain-MGUS was missed. Serum/urine-MASS-FIX detected M-proteins in 18 patients with negative serum/urine-PEL/IFE and serum-FLC, 10 of whom had multiple myeloma or AL amyloidosis, who were mistakenly thought to have complete hematologic response by serum/urine-PEL/IFE and serum-FLC. Nearly half of the AL amyloidosis patients had atypical spectra, which may prove to be a clue to the diagnosis and pathogenesis of the disease. In conclusion, MASS-FIX has a comparable sensitivity with PEL/IFE/FLC methods and can help inform the clinical diagnosis.

ABT-737 is a promising chemotherapeutic agent that promotes apoptosis by acting as a selective BH3 mimetic to neutralize Bcl-2-like family members. One shortcoming with its use is that Mcl-1, a member of the Bcl-2 family, is poorly inhibited by ABT-737 and thus is a major cause of resistance. We performed a short hairpin RNA (shRNA)-based drop-out screen to identify novel genes and pathways that could reverse resistance to ABT-737 treatment in Eµ-myc/Bcl-2 lymphoma cells engineered to rely on endogenous Mcl-1 for survival. Several drug-sensitive shRNAs were identified that were selectively depleted in the presence of ABT-737. Of these, 2 independent shRNAs targeting the RNA/DNA helicase Dhx9 were found to sensitize lymphomas to ABT-737 to an extent comparable to control Mcl-1 shRNAs. Although Dhx9 suppression sensitized both mouse and human cells to ABT-737 treatment, it did so without altering MCL-1 levels. Rather, loss of Dhx9 appeared to activate a p53-dependent apoptotic program, through aggravation of replicative stress, which was found to be both necessary and sufficient for the ABT-737-shDhx9 synthetic lethal relationship.

Mcl-1, a pro-survival member of the Bcl-2 family located at the mitochondrial outer membrane, is subject to constitutive ubiquitylation by the Bcl-2 homology 3-only E3 ligase, Mule/ Lasu1, resulting in rapid steady-state degradation via the proteasome. Insertion of newly synthesized Mcl-1 into the mitochondrial outer membrane is dependent on its C-terminal transmembrane segment, but once inserted, the N terminus of a portion of the Mcl-1 molecules can be subject to proteolytic processing. Remarkably, this processing requires an intact electrochemical potential across the inner membrane. Three lines of evidence directed at the endogenous protein, however, indicate that the resulting Mcl-1ΔN isoform resides in the outer membrane: (i) full-length Mcl-1 and Mcl-1ΔN resist extraction by alkali but are accessible to exogenous protease; (ii) almost the entire populations of Mcl-1 and Mcl-1ΔN are accessible to the membrane-impermeant Cys-reactive agent 4-acetamido-4'- [(iodoacetyl)amino]stilbene-2,2'-disulfonic acid; and (iii) Mcl-1 and Mcl-1ΔN exhibit equivalent chemical cross-linking to Bak in intact mitochondria, an Mcl-1 binding partner located in the outer membrane. In addition to the Mule Bcl-2 homology 3 domain, we show that interaction between Mcl-1 and Mule also requires the extreme N terminus of Mcl-1, which is lacking in Mcl-1ΔN. Thus, Mcl-1ΔN does not interact with Mule, exhibits reduced steady-state ubiquitylation, evades the hyper-rapid steady-state degradation that is observed for full-length Mcl-1 in response to treatments that limit global protein synthesis, and confers resistance to UV stress-induced cell death

Cytoplasmic stress granules (SGs) are specialized regulatory sites of mRNA translation that form under different stress conditions known to inhibit translation initiation. The formation of SG occurs via two pathways; the eukaryotic initiation factor (eIF) 2α phosphorylation-dependent pathway mediated by stress and the eIF2α phosphorylation-independent pathway mediated by inactivation of the translation initiation factors eIF4A and eIF4G. In this study, we investigated the effects of targeting different translation initiation factors and steps in SG formation in HeLa cells. By depleting eIF2α, we demonstrate that reduced levels of the eIF2.GTP.Met-tRNAiMet ternary translation initiation complexes is sufficient to induce SGs. Likewise, reduced levels of eIF4B, eIF4H, or polyA-binding protein, also trigger SG formation. In contrast, depletion of the cap-binding protein eIF4E or preventing its assembly into eIF4F results in modest SG formation. Intriguingly, interfering with the last step of translation initiation by blocking the recruitment of 60S ribosome either with 2-(4-methyl-2,6-dinitroanilino)-N-methylpropionamideis or through depletion of the large ribosomal subunits protein L28 does not induce SG assembly. Our study identifies translation initiation steps and factors involved in SG formation as well as those that can be targeted without induction of SGs.

The Myc/Max/Mad family of transcription factors and the eukaryotic initiation factor 4F (eIF4F) complex play fundamental roles in regulating cell growth, proliferation, differentiation, and oncogenic transformation. eIF4F is involved in the recruitment of ribosomes to mRNAs and is thought to generally be the rate-limiting phase of translation. Here, we show that c-Myc directly activates transcription of the three subunits of eIF4F (eIF4E, eIF4AI, and eIF4GI). These transcriptional effects are mediated through canonical E-boxes (5′CACGTG3′) present in the promoters of these genes. In addition, the c-Myc antagonist Mad1 down-regulates the expression of eIF4F subunits. We also show that MycER activation stimulates protein synthesis at the level of translation initiation. Increased eIF4F levels result in stimulation of c-Myc mRNA translation specifically, as assessed by quantitative reverse transcription–PCR. We use a murine model of lymphomagenesis to show the expression of eIF4F subunits is also up-regulated by c-Myc in vivo. Our results suggest the presence of a feedforward loop involving c-Myc and eIF4F that serves to link transcription and translation and that could contribute to the effects of c-Myc on cell proliferation and neoplastic growth. [Cancer Res 2008;68(13):5326–34]

Two recent studies provide alternative views of the current state and future prospects of southern forests and timber supply: the Southern Forest Resource Assessment (SOFRA) and the Fifth Resources Planning Act Timber Assessment (RPA). Using apparently comparable data but different models and methods, the studies portray futures that in some aspects are quite similar and in others markedly different. This article focuses on what the differences and commonalities between the reports suggest about the key factors that help shape our views of the future of southern timber supply. What inputs and assumptions make important differences in projections of the South's timber supply future? We find that there are five major areas to watch: (i) gross land area shifts from forest to urban and from agriculture to forest (not just net timberland area change); (ii) the sensitivity of pine plantation investments to expected timber prices; (iii) the responsiveness of southern timber demand to prices; (iv) age or date of the starting inventory and the definition of timber harvest (what products are included); and (iv) the basic yield assumptions and the timing of the yield impacts from improved management and timberland area change. South. J. Appl. For. 29(3):123–134.

In recent years much interest has developed about the dynamics of forest type transitions, especially the transitions of land to and from southern pine plantations. This article presents 50-yr-forest type projections developed from two approaches to specifying the type transition matrices. One approach used transition matrices derived with remeasured plot data for six forest types using USDA Forest Service Forest Inventory and Analysis data. These data tracked transitions that occurred either naturally or artificially on inventory plots during one remeasurement cycle. The second approach relied on expert opinion surveys that predicted trends in the future of forest management. The transition matrices were developed from the responses regarding managers' intentions to regenerate stands following harvest. The survey was developed for the 2000 Forest and Rangeland Renewable Resources Planning Act Timber Assessment (2000 RPA). The timber inventories in eight states in the southcentral United States are projected with these methods of handling type transitions, and the results are compared to the 2000 RPA, which used a combination or hybrid approach to type transitioning. All three techniques conclude the area of planted pine is expected to increase well into the future. They are contradictory, however, in predicting the area other forest types will occupy, especially natural pine and upland hardwoods. Projections based on recent history give us one result; projections based on managers' intentions show another. South. J. Appl. For. 27(3):190–197.

DHX9 is an ATP-dependent DEXH box helicase with a multitude of cellular functions. Its ability to unwind both DNA and RNA, as well as aberrant, noncanonical polynucleotide structures, has implicated it in transcriptional and translational regulation, DNA replication and repair, and maintenance of genome stability. We report that loss of DHX9 in primary human fibroblasts results in premature senescence, a state of irreversible growth arrest. This is accompanied by morphological defects, elevation of senescence-associated β-galactosidase levels, and changes in gene expression closely resembling those encountered during replicative (telomere-dependent) senescence. Activation of the p53 signaling pathway was found to be essential to this process. ChIP analysis and investigation of nascent DNA levels revealed that DHX9 is associated with origins of replication and that its suppression leads to a reduction of DNA replication. Our results demonstrate an essential role of DHX9 in DNA replication and normal cell cycle progression.

Many cities have policies encouraging homeowners to plant trees. For these policies to be effective, it is important to understand what motivates a homeowner’s tree-planting decision. Researchers address this question by identifying variables that influence participation in a tree-planting program in Portland, Oregon, U.S. According to the study, homeowners with street trees, and those living in older homes, are more likely to participate in the local program. Homeowners who had owned their homes for longer, and those who live in census-block groups with lower high-school graduation rates, are less likely to participate in the program. Results suggest that tree-planting programs may inadvertently exacerbate environmental inequality.

RNAi combined with next-generation sequencing has proven to be a powerful and cost-effective genetic screening platform in mammalian cells. Still, this technology has its limitations and is incompatible with in situ mutagenesis screens on a genome-wide scale. Using p53 as a proof-of-principle target, we readapted the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR associated 9) genome-editing system to demonstrate the feasibility of this methodology for targeted gene disruption positive selection assays. By using novel “all-in-one” lentiviral and retroviral delivery vectors heterologously expressing both a codon-optimized Cas9 and its synthetic guide RNA (sgRNA), we show robust selection for the CRISPR-modified Trp53 locus following drug treatment. Furthermore, by linking Cas9 expression to GFP fluorescence, we use an “all-in-one” system to track disrupted Trp53 in chemoresistant lymphomas in the Eμ-myc mouse model. Deep sequencing analysis of the tumor-derived endogenous Cas9-modified Trp53 locus revealed a wide spectrum of mutants that were enriched with seemingly limited off-target effects. Taken together, these results establish Cas9 genome editing as a powerful and practical approach for positive in situ genetic screens.