Advancing the Sustainability of US Agriculture through Long-Term Research.

Agriculture in the United States must respond to escalating demands for productivity and efficiency, as well as pressures to improve its stewardship of natural resources. Growing global population and changing diets, combined with a greater societal awareness of agriculture's role in delivering ecosystem services beyond food, feed, fiber, and energy production, require a comprehensive perspective on where and how US agriculture can be sustainably intensified, that is, made more productive without exacerbating local and off-site environmental concerns. The USDA's Long-Term Agroecosystem Research (LTAR) network is composed of 18 locations distributed across the contiguous United States working together to integrate national and local agricultural priorities and advance the sustainable intensification of US agriculture. We explore here the concept of sustainable intensification as a framework for defining strategies to enhance production, environmental, and rural prosperity outcomes from agricultural systems. We also elucidate the diversity of factors that have shaped the past and present conditions of cropland, rangeland, and pastureland agroecosystems represented by the LTAR network and identify priorities for research in the areas of production, resource conservation and environmental quality, and rural prosperity. Ultimately, integrated long-term research on sustainable intensification at the national scale is critical to developing practices and programs that can anticipate and address challenges before they become crises.

Functional Evaluation of Three Manure-Borne Indicator Bacteria Release Models with Multiyear Field Experiment Data.

Modeling the fate and transport of Escherichia coli is of substantial interest because of how this organism serves as an indicator of fecal contamination in microbial water quality assessment. The efficacy of models used to assess the export of E. coli from agricultural fields is dependent, in part, on submodels they utilize to simulate E. coli release from land-applied manure and animal waste. Although several release submodels have been proposed, they have only been evaluated and compared with data from laboratory or small plot E. coli release experiments. Our objective was to evaluate and compare performances of three manure-borne bacteria release submodels at field-scale: exponential release (EM), two-parametric Bradford and Schijven (B-S), and two-parametric Vadas-Kleinman-Sharpley (VKS); each was independently incorporated and tested as a submodel within the export model KINEROS2/STWIR, using E. coli. Dairy manure was uniformly applied via surface broadcasting once a year for six consecutive years on a 0.28 ha experimental field site. Two irrigation events followed each application: the first immediately followed the initial application and the second occurred one week later. Manure and soil samples were collected before and after irrigation, respectively, and manure, soil, and edge-of-field runoff samples were analyzed for E. coli. Model performance was evaluated with the Akaike criterion, coefficients of determination (R2), and root mean squared errors (RMSE) values. The percentage of exported manure-borne E. coli varied from 0.1% to 10% in most cases, generally reflecting the lag time between initiation of irrigation and initiation ofedge-of-field runoff. The export model performed better when using the VKS submodel which was preferred in 55% of cases. The B-S and EM submodels were preferred in 27% and 18% of cases, respectively. Two-parametric submodels were ultimately preferred over the single parameter submodel.

The sensitivity of ecosystem carbon exchange to seasonal precipitation and woody plant encroachment.

Ongoing, widespread increases in woody plant abundance in historical grasslands and savannas (woody encroachment) likely will interact with future precipitation variability to influence seasonal patterns of carbon cycling in water-limited regions. To characterize the effects of woody encroachment on the sensitivity of ecosystem carbon exchange to seasonal rainfall in a semi-arid riparian setting we used flux-duration analysis to compare 2003-growing season NEE data from a riparian grassland and shrubland. Though less seasonally variable than the grassland, shrubland NEE was more responsive to monsoon rains than anticipated. During the 2004-growing season we measured leaf gas exchange and collected leaf tissue for delta(13)C and nitrogen content analysis periodically among three size classes of the dominant woody-plant, Prosopis velutina and the dominant understory species, Sporobolus wrightii, a C(4) bunchgrass, present at the shrubland. We observed size-class and plant functional type independent patterns of seasonal plant performance consistent with greater-than-anticipated sensitivity of NEE in the shrubland. This research highlights the complex interaction between growing-season precipitation, plant-available alluvial groundwater and woody plant abundance governing ecosystem carbon balance in this semi-arid watershed.

The retinoblastoma tumor-suppressor gene, the exception that proves the rule.

The retinoblastoma tumor-suppressor gene (Rb1) is centrally important in cancer research. Mutational inactivation of Rb1 causes the pediatric cancer retinoblastoma, while deregulation of the pathway in which it functions is common in most types of human cancer. The Rb1-encoded protein (pRb) is well known as a general cell cycle regulator, and this activity is critical for pRb-mediated tumor suppression. The main focus of this review, however, is on more recent evidence demonstrating the existence of additional, cell type-specific pRb functions in cellular differentiation and survival. These additional functions are relevant to carcinogenesis suggesting that the net effect of Rb1 loss on the behavior of resulting tumors is highly dependent on biological context. The molecular mechanisms underlying pRb functions are based on the cellular proteins it interacts with and the functional consequences of those interactions. Better insight into pRb-mediated tumor suppression and clinical exploitation of pRb as a therapeutic target will require a global view of the complex, interdependent network of pocket protein complexes that function simultaneously within given tissues.

Cell cycle regulation of c-Jun N-terminal kinase activity at the centrosomes.

The c-Jun N-terminal kinase (JNK), a subgroup of the mitogen-activated protein kinase (MAPK) family of serine/threonine kinases, has established functions in cell growth and apoptosis. While the mechanisms are unclear, JNK has also been also implicated in signaling pathways that initiate cell cycle checkpoints and cell cycle progression. By following the localization of active and inactive JNK during the cell cycle, we have found that the majority of cellular JNK is soluble and present in the cytoplasm and the nucleus. Interestingly, insoluble fractions of JNK are also localized in nuclear and cytoplasmic speckles, and to the centrosomes. While JNK is associated with the centrosome throughout the cell cycle, it is only active at the centrosome from S phase through anaphase. This novel localization of centrosomal JNK is a possible link between JNK-activating stimuli and centrosome or cell cycle events.

The nuclear death domain protein p84N5 activates a G2/M cell cycle checkpoint prior to the onset of apoptosis.

In contrast to extracellular signals, the mechanisms utilized to transduce nuclear apoptotic signals are not well understood. Characterizing these mechanisms is important for predicting how tumors will respond to genotoxic radiation or chemotherapy. The retinoblastoma (Rb) tumor suppressor protein can regulate apoptosis triggered by DNA damage through an unknown mechanism. The nuclear death domain-containing protein p84N5 can induce apoptosis that is inhibited by association with Rb. The pattern of caspase and NF-kappaB activation during p84N5-induced apoptosis is similar to p53-independent cellular responses to DNA damage. One hallmark of this response is the activation of a G(2)/M cell cycle checkpoint. In this report, we characterize the effects of p84N5 on the cell cycle. Expression of p84N5 induces changes in cell cycle distribution and kinetics that are consistent with the activation of a G(2)/M cell cycle checkpoint. Like the radiation-induced checkpoint, caffeine blocks p84N5-induced G(2)/M arrest but not subsequent apoptotic cell death. The p84N5-induced checkpoint is functional in ataxia telangiectasia-mutated kinase-deficient cells. We conclude that p84N5 induces an ataxia telangiectasia-mutated kinase (ATM)-independent, caffeine-sensitive G(2)/M cell cycle arrest prior to the onset of apoptosis. This conclusion is consistent with the hypotheses that p84N5 functions in an Rb-regulated cellular response that is similar to that triggered by DNA damage.

Adenovirus-mediated N5 gene transfer inhibits tumor cell proliferation by induction of apoptosis.

Gene therapy designed to initiate apoptotic cell death provides a potentially effective method to treat cancer. A prerequisite for this approach is the identification of genes that function in distinct apoptotic pathways. Although apoptotic pathways initiated by receptors such as tumor necrosis factor receptor-1 are well characterized, little is known about apoptotic pathways initiated within the nucleus in response to genotoxic stress. We have demonstrated previously that the nuclear, death domain-containing protein p84N5 can induce apoptosis upon transfection into cells, suggesting that it may play a role in an apoptotic pathway initiated within the nucleus. To test the possibility that N5 could be used in the gene therapy of cancer, we have generated a recombinant adenovirus engineered to express N5 and tested the effects of viral infection on the growth and tumorigenicity of tumor cells. N5 adenovirus infection significantly reduced the proliferation and tumorigenicity of breast, ovarian, and osteosarcoma tumor cell lines. Reduced proliferation and tumorigenicity were mediated by an induction of apoptosis as indicated by DNA fragmentation in infected cells. The results suggest that the N5 cDNA is a candidate for the gene therapy of cancer.

Apoptosis induced by the nuclear death domain protein p84N5 is associated with caspase-6 and NF-kappa B activation.

Although the mechanisms involved in responses to extracellular or mitochondrial apoptotic signals have received considerable attention, the mechanisms utilized within the nucleus to transduce apoptotic signals are not well understood. We have characterized apoptosis induced by the nuclear death domain-containing protein p84N5. Adenovirus-mediated N5 gene transfer or transfection of p84N5 expression vectors induces apoptosis in tumor cell lines with nearly 100% efficiency as indicated by cellular morphology, DNA fragmentation, and annexin V staining. Using peptide substrates and Western blotting, we have determined that N5-induced apoptosis is initially accompanied by activation of caspase-6. Activation of caspases-3 and -9 does not peak until 3 days after the peak of caspase-6 activity. Expression of p84N5 also leads to activation of NF-kappaB as indicated by nuclear translocation of p65RelA and transcriptional activation of a NF-kappaB-dependent reporter promoter. Changes in the relative expression level of Bcl-2 family proteins, including Bak and Bcl-Xs, are also observed during p84N5-induced apoptosis. Finally, we demonstrate that p84N5-induced apoptosis does not require p53 and is not inhibited by p53 coexpression. We propose that p84N5 is involved in an apoptotic pathway distinct from those triggered by death domain-containing receptors or by p53.

Glutamic acid mutagenesis of retinoblastoma protein phosphorylation sites has diverse effects on function.

The retinoblastoma tumor suppressor gene (Rb) has many functions within the cell including regulation of transcription, differentiation, apoptosis, and the cell cycle. Regulation of these functions is mediated by phosphorylation at as many as 16 cyclin-dependent kinase (CDK) phosphorylation sites in vivo. The contribution of these sites to the regulation of the various Rb functions is not well understood. To characterize the effect of phosphorylation at these sites, we systematically mutagenized the serines or threonines to glutamic acid. Thirty-five mutants with different combinations of modified phosphorylation sites were assayed for their ability to arrest the cell cycle and for their potential to induce differentiation. Only the most highly substituted mutants failed to arrest cell cycle progression. However, mutants with as few as four modified phosphorylation sites were unable to promote differentiation. Other mutants had increased activity in this assay. We conclude that modification of Rb phosphorylation sites can increase or decrease protein activity, that different Rb functions can be regulated independently by distinct combinations of sites, and that the effects of modification at any one site are context dependent.

Apoptosis induced by the nuclear death domain protein p84N5 is inhibited by association with Rb protein.

Rb protein inhibits both cell cycle progression and apoptosis. Interaction of specific cellular proteins, including E2F1, with Rb C-terminal domains mediates cell cycle regulation. In contrast, the nuclear N5 protein associates with an Rb N-terminal domain with unknown function. The N5 protein contains a region of sequence similarity to the death domain of proteins involved in apoptotic signaling. We demonstrate here that forced N5 expression potently induces apoptosis in several tumor cell lines. Mutation of conserved residues within the death domain homology compromise N5-induced apoptosis, suggesting that it is required for normal function. Endogenous N5 protein is specifically altered in apoptotic cells treated with ionizing radiation. Furthermore, dominant interfering death domain mutants compromise cellular responses to ionizing radiation. Finally, physical association with Rb protein inhibits N5-induced apoptosis. We propose that N5 protein plays a role in the regulation of apoptosis and that Rb directly coordinates cell proliferation and apoptosis by binding specific proteins involved in each process through distinct protein binding domains.

Histone H3 phosphorylation is required for the initiation, but not maintenance, of mammalian chromosome condensation.

The temporal and spatial patterns of histone H3 phosphorylation implicate a specific role for this modification in mammalian chromosome condensation. Cells arrest in late G2 when H3 phosphorylation is competitively inhibited by microinjecting excess substrate at mid-S-phase, suggesting a requirement for activity of the kinase that phosphorylates H3 during the initiation of chromosome condensation and entry into mitosis. Basal levels of phosphorylated H3 increase primarily in late-replicating/early-condensing heterochromatin both during G2 and when premature chromosome condensation is induced. The prematurely condensed state induced by okadaic acid treatment during S-phase culminates with H3 phosphorylation throughout the chromatin, but in an absence of mitotic chromosome morphology, indicating that the phosphorylation of H3 is not sufficient for complete condensation. Mild hypotonic treatment of cells arrested in mitosis results in the dephosphorylation of H3 without a cytological loss of chromosome compaction. Hypotonic-treated cells, however, complete mitosis only when H3 is phosphorylated. These observations suggest that H3 phosphorylation is required for cell cycle progression and specifically for the changes in chromatin structure incurred during chromosome condensation.

Infrequent mutation of the p16/MTS1 gene and overexpression of cyclin-dependent kinase 4 in human primary soft-tissue sarcoma.

The pl6INK4a/MTS1 (p16) gene encodes a specific inhibitor of cyclin-dependent kinase (CDK)4 and CDK6. The p16 gene is frequently mutated or deleted in many types of cancer cell lines as well as in certain types of primary tumors. p16 knockout mice are viable but predisposed to sarcoma and B-cell lymphoma. To investigate the role of p16 in human soft-tissue sarcoma tumor progression, we examined the p16 gene by Southern blot analysis and PCR sequencing in 30 pairs of primary soft-tissue sarcomas and autologous normal tissue. Only one tumor sample showed possible rearrangement of the p16 gene. In contrast, Western blot analysis of the p16 protein in 20 pairs of samples showed decreased p16 expression in only 20% of the tumors but elevated p16 expression in 40% of the tumors when compared with the autologous normal controls. Overexpression of p16 was not concomitant with loss of the RB protein as is found in several other types of cancers, because more than one-half of the tumors with increased p16 expression also had high levels of RB protein. On the other hand, the p16 target protein CDK4 was overexpressed in at least 60% of the tumors. In the majority of cases, CDK4 overexpression accompanied elevated p16 and/or RB levels. Our results suggest that: (a) alteration of the p16 gene is infrequent in primary soft-tissue sarcoma; (b) Cdk4 may act as an oncogene in soft-tissue sarcoma; and (c) elevated p16 and RB levels might be the result of compensatory up-regulation of these proteins to counteract CDK4 overexpression in these tumors. Our results also suggest that it is more informative to examine aberrations in the "p16-CDK4/cyclin D-RB" pathway than to selectively examine individual components in this pathway when investigating genetic changes involved in human malignancy.

S-Phase entry upon ectopic expression of G1 cyclin-dependent kinases in the absence of retinoblastoma protein phosphorylation.

In mammalian cells, the retinoblastoma protein (Rb) is thought to negatively regulate progression through the G1 phase of the cell cycle by its association with the transcription factor E2F [1-3]. Rb-E2F complexes suppress transcription of genes required for DNA synthesis ([4], reviewed in [3,5]), and the prevailing view is that phosphorylation of Rb by complexes of cyclin-dependent kinases (Cdks) and their regulatory cyclin subunits, and the subsequent release of active E2F, is required for S-phase entry [1-3]. This view is based, in part, on the fact that ectopic expression of cyclin-Cdks leads to Rb phosphorylation and that this modification correlates with S-phase entry [6-8]. In Drosophila, however, cyclin E expression can bypass a requirement for E2F, suggesting that cyclins may activate replication independently of the Rb/E2F pathway [9]. We sought to examine whether Rb phosphorylation is a prerequisite for S-phase entry in Rb-deficient SAOS-2 osteosarcoma cells, using a commonly used cotransfection assay [6-8,10]. We find that a G1 arrest in SAOS-2 cells mediated by an Rb mutant lacking all 14 consensus Cdk phosphorylation sites is bypassed by coexpressing G1-specific E-type or D-type cyclin-Cdk complexes, and that injection of purified cyclin-Cdks during G1 accelerates S-phase entry. Our results indicate that Rb phosphorylation is not essential for S-phase entry when G1 cyclin-Cdks are overexpressed, and that other substrates of these kinases can be rate-limiting for the G1 to S-phase transition. These data also reveal that the SAOS-2 cotransfection assay is complicated by Rb-independent effects of the coexpressed Cdks.

Cyclin D1/Cdk4 regulates retinoblastoma protein-mediated cell cycle arrest by site-specific phosphorylation.

The retinoblastoma protein (pRb) inhibits progression through the cell cycle. Although pRb is phosphorylated when G1 cyclin-dependent kinases (Cdks) are active, the mechanisms underlying pRb regulation are unknown. In vitro phosphorylation by cyclin D1/Cdk4 leads to inactivation of pRb in a microinjection-based in vivo cell cycle assay. In contrast, phosphorylation of pRb by Cdk2 or Cdk3 in complexes with A- or E-type cyclins is not sufficient to inactivate pRb function in this assay, despite extensive phosphorylation and conversion to a slowly migrating "hyperphosphorylated form." The differential effects of phosphorylation on pRb function coincide with modification of distinct sets of sites. Serine 795 is phosphorylated efficiently by Cdk4, even in the absence of an intact LXCXE motif in cyclin D, but not by Cdk2 or Cdk3. Mutation of serine 795 to alanine prevents pRb inactivation by Cdk4 phosphorylation in the microinjection assay. This study identifies a residue whose phosphorylation is critical for inactivation of pRb-mediated growth suppression, and it indicates that hyperphosphorylation and inactivation of pRb are not necessarily synonymous.

The human retinoblastoma gene product suppresses ceramide-induced apoptosis in human bladder tumor cells.

The retinoblastoma gene product, Rb, has previously been implicated as an obligatory component in the antiproliferative effects mediated by the lipid second messenger, ceramide. We have evaluated both the apoptotic effects and the effects on cell cycle distribution of the exogenous cell-permeable ceramide, N-hexanoyl-D-sphingosine, in an Rb-null human bladder tumor cell line, 5637, as well as in retrovirally infected, Rb(+) clones derived therefrom. These cell lines demonstrated comparable sensitivity to N-hexanoyl-D-sphingosine in a neutral red dye uptake assay. Exposure of the Rb-null parental cell line to 20 microM N-hexanoyl-D-sphingosine for 24 h resulted in a classical pattern of DNA fragmentation that was accompanied by apoptotic nuclear morphological alterations. In contrast, the Rb(+) clones demonstrated suppression of DNA fragmentation in response to N-hexanoyl-D-sphingosine. Similarly, the frequency and degree of alteration of nuclear morphology in Rb(+) cells was also suppressed. Flow cytometric analysis of the parental and infected clones indicated that expression of Rb was without effect on their cell cycle distribution, with or without exposure to N-hexanoyl-D-sphingosine for 25 h; tunel assay confirmed that in this time frame apoptotic cells were far less frequent in the Rb(+) clones than in the parental 5637 cells. Human tumor cell lines derived from three other histological origins, breast and prostatic carcinomas and osteogenic sarcoma, also demonstrated very similar cytotoxic sensitivities to N-hexanoyl-D-sphingosine, irrespective of the expression of Rb. We conclude that Rb is not required for ceramide-induced apoptosis and that Rb can actually inhibit the DNA fragmentation and nuclear morphological changes associated with classical apoptosis.

G1 arrest and down-regulation of cyclin E/cyclin-dependent kinase 2 by the protein kinase inhibitor staurosporine are dependent on the retinoblastoma protein in the bladder carcinoma cell line 5637.

The protein kinase inhibitor staurosporine has been shown to induce G1 phase arrest in normal cells but not in most transformed cells. Staurosporine did not induce G1 phase arrest in the bladder carcinoma cell line 5637 that lacks a functional retinoblastoma protein (pRB-). However, when infected with a pRB-expressing retrovirus [Goodrich, D. W., Chen, Y., Scully, P. & Lee, W.-H. (1992) Cancer Res. 52, 1968-1973], these cells, now pRB+, were arrested by staurosporine in G1 phase. This arrest was accompanied by the accumulation of hypophosphorylated pRB. In both the pRB+ and pRB- cells, cyclin D1-associated kinase activities were reduced on staurosporine treatment. In contrast, cyclin-dependent kinase (CDK) 2 and cyclin E/CDK2 activities were inhibited only in pRB+ cells. Staurosporine treatment did not cause reductions in the protein levels of CDK4, cyclin D1, CDK2, or cyclin E. The CDK inhibitor proteins p21(Waf1/Cip1) and p27 (Kip1) levels increased in staurosporine-treated cells. Immunoprecipitation of CDK2, cyclin E, and p2l from staurosporine-treated pRB+ cells revealed a 2.5- to 3-fold higher ratio of p2l bound to CDK2 compared with staurosporine-treated pRB- cells. In pRB+ cells, p2l was preferentially associated with Thrl6O phosphorylated active CDK2. In pRB- cells, however, p2l was bound preferentially to the unphosphorylated, inactive form of CDK2 even though the phosphorylated form was abundant. This is the first evidence suggesting that G1 arrest by 4 nM staurosporine is dependent on a functional pRB protein. Cell cycle arrest at the pRB- dependent checkpoint may prevent activation of cyclin E/CDK2 by stabilizing its interaction with inhibitor proteins p2l and p27.

Molecular characterization of the retinoblastoma susceptibility gene.

Retinoblastoma is recognized as a hereditary cancer. Genetic and epidemiological analysis of the disease has been incorporated into a two-hit mutational inactivation hypothesis of the origin of retinoblastoma. The molecular cloning and characterization of the retinoblastoma gene and gene product has allowed a critical testing of this two-hit hypothesis. All the predications of the model have been born out by experiment so far. These include inheritance of one mutated RB allele as the origin of hereditary retinoblastoma, subsequent loss of the remaining allele upon tumorigenesis, the involvement of the same RB gene in both sporadic and hereditary retinoblastoma, the somatic mutation of both RB alleles in sporadic retinoblastoma, the lack of RB expression in any retinoblastoma yet examined, and the recessiveness of mutated RB alleles. The RB gene exhibits functional properties consistent with its role as a suppressor of tumor formation. For example, re-expression of RB in tumor cells lacking endogenous RB leads to a loss of tumorigenic properties. RB protein can also inhibit progression through the cell division cycle, and it physically and/or functionally interacts with important cell cycle regulatory molecules. Although confirmation of the two-hit hypothesis seems complete, we can not rule out the possibility that other genes are involved in the genesis of this tumor. For example, there seems to be variable resistance to tumor development even in patients inheriting retinoblastoma susceptibility. Further, heterozygous RB null mice do not develop retinoblastoma, but develop a characteristic brain tumor instead. The molecular isolation of the RB gene is an important achievement in research on cancer. For the first time, it has become possible to examine, at the molecular level, genes that inhibit the growth of tumor cells. The precise mechanism of action of RB is unknown, but a broad outline is beginning to emerge. RB seems to negatively influence tumor cell growth by participating in regulation of the cell division cycle. RB has also been implicated in differentiation; its effect on the cell division cycle and its effects on differentiation may be different manifestations of the same function. Since RB is involved in oncogenesis, gene regulation, and cellular differentiation, it is obviously an attractive gene for intense study; understanding the function and mechanism of action of RB will impact the understanding of many, important cell processes.

Abrogation by c-myc of G1 phase arrest induced by RB protein but not by p53.

Inactivating mutations of the retinoblastoma gene (RB) are found in a wide variety of tumour cells. Replacement of wild-type RB can suppress the tumorigenicity of some of these cells, suggesting that the RB protein (Rb) may negatively regulate cell growth. As activation of c-myc expression promotes cell proliferation and blocks differentiation, it may positively regulate cell growth. The c-myc protein is localized in the nucleus and can physically associate with RB protein in vitro, hence c-myc may functionally antagonize RB function. Microinjection of Rb in G1 phase reversibly arrests cell-cycle progression. Here we co-inject RB protein with c-myc, EJ-ras, c-fos or c-jun protein. Co-injection of c-myc, but not EJ-ras, c-fos or c-jun, inhibits the ability of Rb to arrest the cell cycle. The c-myc does not inhibit the activity of another tumour supressor, p53 (ref. 12). Thus, c-myc and RB specifically antagonize one another in the cell.