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The C-terminal repeat domain (CTD) of RNA polymerase II (RNAPII) is an intrinsically unstructured extension of the enzyme's largest subunit, RPB1. The CTD is composed of a tandem array of seven amino acid repeats with the consensus sequence Y1S2P3T4S5P6S7; the number of heptad repeats varies from organism to organism and appears to correlate with genomic complexity (Corden 1990). Although dispensable for polymerase activity in vitro, the CTD is conserved throughout evolution and is essential to life (Zehring et al. 1988). The CTD's function is to coordinate transcription with nuclear processes such as mRNA processing and chromatin modification; it fulfills this role by serving as a selective binding scaffold for nuclear factors (for review, see Phatnani and Greenleaf 2006). The binding specificity of the CTD for particular factors is determined by its phosphorylation state, which varies during the transcription cycle; Ser2, Ser5, and, more recently, Ser7 of the heptad repeat have been identified as the primary targets of phosphorylation (Phatnani and Greenleaf 2006; Chapman et al. 2007; Egloff et al. 2007). Initiated and early transcribing polymerases are thought to be phosphorylated at Ser5 positions in the CTD repeats, whereas actively elongating polymerases carry phosphates on both Ser2 and Ser5 residues. Toward the 3′ end of pre-mRNA transcription units, Ser2 phosphorylation often appears to predominate (cf. Phatnani and Greenleaf 2006; Rahl et al. 2010). CTD kinases in yeast and metazoa The phosphorylation of CTD Ser5 residues during initiation and early transcription is mediated by the TFIIH CTD kinase subunit: Kin28 in yeast, and CDK7 in metazoans (Komarnitsky et al. 2000; Schroeder et al. 2000). The majority of Ser2 phosphorylation on productively elongating RNAPII in Saccharomyces cerevisiae (Sc) appears to be catalyzed by CTDK-I (Buratowski 2009; Qiu et al. 2009), a three-subunit enzyme consisting of Ctk1 (a CDK homolog), Ctk2 (a cyclin homolog), and Ctk3 (function unknown) (Lee and Greenleaf 1991; Sterner et al. 1995). Although it is responsible for the bulk of Ser2 phosphorylation in vivo, the Ctk1-containing enzyme is not the only elongation phase kinase in yeast; it coexists with the essential Bur1 kinase (CDK/cyclin pair = Bur1/Bur2) (Yao et al. 2000). While it has been proposed that the Bur1 kinase phosphorylates the transcription elongation factor subunit SPT5 rather than the CTD of Rpb1 (Zhou et al. 2009), recent evidence suggests that the situation is more complex, and that, in addition to acting on SPT5, the Bur1 kinase phosphorylates Ser2 positions in the CTD (Liu et al. 2009; Qiu et al. 2009), possibly stimulating subsequent phosphorylation by Ctk1. A similar pair of Ser2 CTD kinases is also present in the fission yeast Schizzosaccharomyces pombe (Sp): Lsk1, the Ctk1 ortholog in Sp, phosphorylates Ser2 positions in the CTD (Karagiannis and Balasubramanian 2007; Coudreuse et al. 2010), whereas SpCDK9, the Bur1 ortholog, phosphorylates both Rpb1 (on its CTD) and Spt5 (Viladevall et al. 2009). With respect to the principal Ser2 kinase in metazoa, the situation has been less clear cut. It is currently thought that there is only one Ser2 CTD kinase in higher organisms: P-TEFb (consisting of CDK9 and a cyclin, usually cyclin T) (e.g., see Peterlin and Price 2006). P-TEFb is able to phosphorylate both the CTD and the elongation factor subunit SPT5 (Kim and Sharp 2001). The dual functionality of CDK9, coupled with its equal sequence similarity to both Bur1 and Ctk1, has led to the assumption that CDK9 reconstitutes the activities of both Bur1 and Ctk1 in higher eukaryotes (Wood and Shilatifard 2006). On the other hand, two independent molecular evolution studies concluded that Sc Bur1 is the closest Sc relative of metazoan CDK9 proteins, while Sc Ctk1 is closer to a set of metazoan CDK proteins that are largely unstudied (Liu and Kipreos 2000; Guo and Stiller 2004): the “Ctk1” group (Supplemental Fig. S1). The genomes of Drosophila melanogaster (Dm) and Caenorhabditis elegans (Ce) each encode one member of the Ctk1 group (genes CG7597 and B0285.1, respectively), while the genome of Homo sapiens (Hs) encodes two (genes CRKRS and CDC2L5; see Supplemental Fig S1). The human “Ctk1” proteins have been renamed recently CDK12 and CDK13 (Chen et al. 2006, 2007). We refer to them as hCDK12 and hCDK13, and to the Dm protein as dCDK12. The evolutionary studies thus suggest that the metazoan ortholog of Ctk1 in Drosophila is dCDK12 and in humans is one or both of the isozyme pair, hCDK12 + hCDK13. Also, the evolutionary arguments and the recent experimental work mentioned above both suggest that the metazoan ortholog of Bur1 is CDK9. We tested these suggestions with a set of diverse experiments that lead us to conclude that, indeed, the Drosophila ortholog of yeast Ctk1 is dCDK12 (CG7597), and the human ortholog is most likely hCDK12. Conversely, we describe other experiments supporting the idea that the metazoan ortholog of yeast Bur1 is CDK9. Because the metazoan orthologs of yeast Ctk1 have not been studied previously as CTD kinases, our findings open the door to novel studies of a vast array of transcription-related events in metazoa that are critical to many aspects of proper gene expression and other nuclear functions.

Regulation of the expression of the human immunodeficiency virus (HIV) genome is accomplished in large part by controlling transcription elongation. The viral protein Tat hijacks the host cell’s RNA polymerase II elongation control machinery through interaction with the positive transcription elongation factor, P-TEFb, and directs the factor to promote productive elongation of HIV mRNA. Here we describe the crystal structure of the Tat·P-TEFb complex containing HIV-1 Tat, human Cdk9 (also known as CDK9), and human cyclin T1 (also known as CCNT1). Tat adopts a structure complementary to the surface of P-TEFb and makes extensive contacts, mainly with the cyclin T1 subunit of P-TEFb, but also with the T-loop of the Cdk9 subunit. The structure provides a plausible explanation for the tolerance of Tat to sequence variations at certain sites. Importantly, Tat induces significant conformational changes in P-TEFb. This finding lays a foundation for the design of compounds that would specifically inhibit the Tat·P-TEFb complex and block HIV replication. The Tat protein of the human immunodeficiency virus (HIV) has been a target for structural studies for many years, with a view to possible therapeutic intervention. Tat is active early in an infection, hijacking the host's positive transcription elongation factor, P-TEFb. The latter, unusually for a host protein, is therefore also a potential drug target. Tahirov et al. report the first crystal structure for HIV Tat in complex with P-TEFb. The 2.1-A crystal structure shows that, although the interaction interface between Tat and P-TEFb is large, Tat binding changes the structure of P-TEFb. This points to possible opportunities for developing inhibitors that block only the form of P-TEFb that is used by the virus. Here the 2.1 A crystal structure of human immunodeficiency virus (HIV) Tat protein complexed with the positive transcription elongation factor P-TEFb is reported. This shows that Tat binding changes the structure of P-TEFb, which may suggest opportunities for developing inhibitors that block only the form of P-TEFb used by the virus.

Purpose Liver metastases are the principal cause of death in patients with advanced colorectal cancer (CRC). Irinotecan is a chemotherapeutic agent used in the treatment of CRC and has demonstrated synergistic potential when used with radiation. Radioembolization with yttrium-90 microspheres has demonstrated increased response and survival rates when given with fluorouracil chemotherapy. This study's goal was to evaluate the maximum-tolerated dose of concomitant irinotecan and radioembolization in fluorouracil-refractory patients with CRC hepatic metastases. Patients and Methods Twenty-five irinotecan-naïve patients who had experienced relapse after previous chemotherapy were enrolled onto three dose-escalating groups. Irinotecan was administered at 50, 75, or 100 mg/m2 on days 1 and 8 of a 3-week cycle for the first two cycles, and full irinotecan doses (ie, 100 mg/m2) were administered during cycles 3 to 9. Radioembolization was administered during the first chemotherapy cycle. Results Most patients experienced acute, self-limiting abdominal pain and nausea. Mild lethargy and anorexia were common. Grades 3 to 4 events were seen in three of six patients at 50 mg/m2 (obstructive jaundice, thrombocytopenia, diarrhea), in five of 13 patients at 75 mg/m2 (neutropenia, leukopenia, thrombocytopenia, elevated alkaline phosphatase, abdominal pain, ascites, fatigue) and in four of six patients at 100 mg/m2 (diarrhea, deep vein thrombosis, constipation, leukopenia). Eleven (48%) of 23 patients had a partial response, and nine patients (39%) had stable disease. The median progression-free survival was 6.0 months; the median survival was 12.2 months. Conclusion Concomitant use of radioembolization plus irinotecan did not reach a maximum-tolerated dose. The recommended dose of irinotecan in this setting is 100 mg/m2 on days 1 and 8 of a 3-week cycle.

The elongation phase of transcription by RNA polymerase II (RNAP II) is tightly controlled by a large number of transcription elongation factors. Here we describe experimental approaches for the isolation of RNAPII elongation complexes in vitro and the use of these complexes in the examination of the function of a variety of factors. The methods start with formation of elongation complexes on DNA templates immobilized to paramagnetic beads. Elongation is halted by removing the nucleotides and the ternary elongation complexes are then stripped of factors by a high salt wash. The effect of any factor or mixture of factors on elongation is determined by adding the factor(s) along with nucleotides and observing the change in the pattern of RNAs generated. Association of a factor with elongation complexes can be examined using an elongation complex electrophoretic mobility shift assay (EC-EMSA) in which elongation complexes that have been liberated from the beads are analyzed on a native gel. Besides being used to dissect the mechanisms of elongation control, these experimental systems are useful for analyzing the function of termination factors and mRNA processing factors. Together these experimental systems permit detailed characterization of the molecular mechanisms of elongation, termination, and mRNA processing factors by providing information concerning both physical interactions with and functional consequences of the factors on RNAPII elongation complexes.

The establishment of professional anthropology is contrasted with the flawed limits and freedom of early self-trained anthropologists working outside of the academy. The work of ethnographer and linguist Jaime de Angulo and photographer Edward S. Curtis are oppositional examples of early 20th century self-trained anthropologically informed field research. While Curtis's career illustrates how work outside of academic anthropological circles often failed to document Indian culture, de Angulo's work provides an example of a brilliant scholar producing innovative, high quality work that would have been difficult to produce under the strictures of early 20th century academic life.

Recent global analyses have determined that many Drosophila and human genes have engaged polymerase molecules trapped immediately downstream of promoters. These results strongly implicate RNA polymerase II elongation control as a major regulator of differentiation and development.

This is the second part of a two-part article by David Price examining how research on stress under Human Ecology Fund sponsorship found its way into the CIA 's Kubark interrogation manual (for Part 1 see our June issue). This issue of ANTHROPOLOGY TODAY also features a short comment by Roberto Gonzalez on the use of Ralph Patai's The Arab mind in training interrogators who worked in Iraq, including at Abu Ghraib (p. 23). See also news, p. 28, for a pledge initiated by the Network of Concerned Anthropologists in response to anthropologists ' concerns around this issue.

The positive transcription elongation factor, P-TEFb, controls the fraction of initiated RNA polymerase II molecules that enter into the productive mode of elongation necessary to generate mRNAs. To better understand the mechanism of this transition into productive elongation we optimized a defined in vitro transcription system and compared results obtained with it to those obtained with a crude system. We found that controlling the function of TFIIF is a key aspect of RNA polymerase II elongation control. Before P-TEFb function, early elongation complexes under the control of negative factors are completely unresponsive to the robust elongation stimulatory activity of TFIIF. P-TEFb-mediated phosphorylation events, targeting the elongation complex containing DSIF and NELF, reverse the negative effect of DSIF and NELF and simultaneously facilitate the action of TFIIF. We also found that productive elongation complexes are completely resistant to negative elongation factors. Our data suggest that an additional factor(s) is involved in establishing the unique resistance activities of the elongation complexes before and after P-TEFb function. Furthermore, we provide evidence for the existence of another positive activity required for efficient function of P-TEFb. A model of the mechanism of P-TEFb-mediated elongation control is proposed in which P-TEFb induces the transition into productive elongation by changing the accessibility of elongation factors to elongation complexes. Our results have uncovered important properties of elongation complexes that allow a more complete understanding of how P-TEFb controls the elongation phases of transcription by RNA polymerase II.

Basal transcription of the HIV LTR is highly repressed and requires Tat to recruit the positive transcription elongation factor, P-TEFb, which functions to promote the transition of RNA polymerase II from abortive to productive elongation. P-TEFb is found in two forms in cells, a free, active form and a large, inactive complex that also contains 7SK RNA and HEXIM1 or HEXIM2. Here we show that HIV infection of cells led to the release of P-TEFb from the large form. Consistent with Tat being the cause of this effect, transfection of a FLAG-tagged Tat in 293T cells caused a dramatic shift of P-TEFb out of the large form to a smaller form containing Tat. In vitro, Tat competed with HEXIM1 for binding to 7SK, blocked the formation of the P-TEFb–HEXIM1–7SK complex, and caused the release P-TEFb from a pre-formed P-TEFb–HEXIM1–7SK complex. These findings indicate that Tat can acquire P-TEFb from the large form. In addition, we found that HEXIM1 binds tightly to the HIV 5′ UTR containing TAR and recruits and inhibits P-TEFb activity. This suggests that in the absence of Tat, HEXIM1 may bind to TAR and repress transcription elongation of the HIV LTR.

P-TEFb regulates eukaryotic gene expression at the level of transcription elongation, and is itself controlled by the reversible association of 7SK RNA and an RNA-binding protein HEXIM1 or HEXIM2. In an effort to determine the minimal region of 7SK needed to interact with HEXIM1 in vitro, we found that an oligo comprised of nucleotides 10–48 sufficed. A bid to further narrow down the minimal region of 7SK led to a surprising finding that HEXIM1 binds to double-stranded RNA in a sequence-independent manner. Both dsRNA and 7SK (10–48), but not dsDNA, competed efficiently with full-length 7SK for HEXIM1 binding in vitro. Upon binding dsRNA, a large conformational change was observed in HEXIM1 that allowed the recruitment and inhibition of P-TEFb. Both subcellular fractionation and immunofluorescence demonstrated that, while most HEXIM1 is found in the nucleus, a significant fraction is found in the cytoplasm. Immunoprecipitation experiments demonstrated that both nuclear and cytoplasmic HEXIM1 is associated with RNA. Interestingly, the one microRNA examined (mir-16) was found in HEXIM1 immunoprecipitates, while the small nuclear RNAs, U6 and U2, were not. Our study illuminates novel properties of HEXIM1 both in vitro and in vivo, and suggests that HEXIM1 may be involved in other nuclear and cytoplasmic processes besides controlling P-TEFb.

Background This prospective, open-label phase II study assessed the impact of liver-directed therapy with selective internal radiation therapy (SIRT) and systemic chemotherapy on progression-free survival (PFS) in liver-dominant metastatic pancreatic adenocarcinoma. Methods Patients received yttrium-90-labelled (90Y) resin microspheres (SIR-Spheres; Sirtex Medical Limited, Sydney, Australia) as a single procedure on day 2 of the first weekly cycle of 5-fluorouracil (5FU; 600 mg/m2) with the option to switch to gemcitabine (1000 mg/m2) after 8 weeks of 5FU. Statistical analysis was conducted using Microsoft Excel (Microsoft Corporation, Redmond, Washington, USA). The primary endpoint of the study was PFS in the liver, with a median of ≥16 weeks defined as the threshold for clinical significance. PFS and overall survival (OS) were summarised by the Kaplan-Meier method using non-parametric estimates of the survivor function. Results Fourteen eligible patients were enrolled; ten had primary tumour in situ and eight had liver-only metastases. Patients received a median 90Y activity of 1.1 GBq and 8 weekly doses of 5FU; seven patients received a median of two doses of gemcitabine. Disease control in the liver was 93 % (two confirmed partial responses [PR], one unconfirmed PR, ten stable disease). Median reduction in cancer antigen 19–9 was 72 %. Median PFS was 5.2 months in the liver, which met the primary endpoint of the study, and 4.4 months at any site. PFS was prolonged in those with a resected primary compared with patients with primary in situ (median 7.8 vs. 3.4 months; p = 0.017). Median OS was 5.5 months overall and 13.6 months in patients with a resected primary. Grade 3/4 adverse events occurred in eight (57 %) patients during days 0–60. There was one sudden death and another patient who died from possible treatment-related liver failure 7.0 months after SIRT. Conclusions SIRT and chemotherapy appears to be an effective treatment for liver metastases from pancreatic cancer, likely to be of most benefit in selected patients with a resected primary tumour and liver only disease. Significant toxicity was observed and the safety of this approach in patients with metastatic pancreatic cancer will need to be confirmed in subsequent studies. Further study is warranted with SIRT and modern chemotherapies. Trial registration ACTRN12606000015549 Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1822-8) contains supplementary material, which is available to authorized users.

There is an error in Fig 2 that appears to have occurred during the preparation of files after the manuscript was accepted. In Fig 2B, the blot for Brd4 incorrectly appears as a duplicate of P-Brd4. The authors have provided a corrected version of Fig 2 here. Fig 2 Brd4 occupancy and expression in different cells.

The positive transcription elongation factor b (P-TEFb) is a cyclin-dependent kinase that controls the elongation phase of transcription by RNA polymerase II (RNAPII). This process is made possible by the reversal of effects of negative elongation factors that include NELF and DSIF. In complex organisms, elongation control is critical for the regulated expression of most genes. In those organisms, the function of P-TEFb is influenced negatively by HEXIM proteins and 7SK snRNA and positively by a variety of recruiting factors. Phylogenetic analyses of the components of the human elongation control machinery indicate that the number of mechanisms utilized to regulate P-TEFb function increased as organisms developed more complex developmental patterns.

Transcription elongation of eukaryotic genes by RNA polymerase II depends on the positive transcription elongation factor b (P-TEFb). When sequestered into the large complex, P-TEFb kinase activity is inhibited by the coordinate actions of 7SK small nuclear RNA (7SK snRNA) and hexamethylene bisacetamide (HMBA)-induced protein 1 (HEXIM1). We found that the basic region in HEXIM1 directs its nuclear import via two monopartite and two bipartite nuclear localization sequences. Moreover, the arginine-rich motif within it is essential for its binding to 7SK snRNA, P-TEFb, and inhibition of transcription. Notably, the basic region interacts with the adjacent acidic regions in the absence of RNA. The removal of the positive or negative charges from these regions in HEXIM1 leads to its sequestration into the large complex and inhibition of transcription independently of the arginine-rich motif. Finally, the removal of the negative charges from HEXIM1 results in its subnuclear localization into nuclear speckles. We propose a model where the interplay between 7SK snRNA and oppositely charged regions in HEXIM1 direct its binding to P-TEFb and subcellular localization that culminates in the inhibition of transcription.

Cleavage and polyadenylation define the 3' ends of almost all eukaryotic mRNAs and are thought to occur during transcription. We describe a human in vitro system utilizing an immobilized template, in which transcripts in RNA polymerase II elongation complexes are efficiently cleaved and polyadenylated. Because the cleavage rate of free RNA is much slower, we conclude that cleavage is functionally coupled to transcription. Inhibition of positive transcription elongation factor b (P-TEFb) had only a modest negative effect on cleavage, as long as transcripts were long enough to contain the polyadenylation signal. In contrast, removal of the carboxyl-terminal domain of the large subunit of RNA polymerase II had a dramatic negative effect on cleavage. Unexpectedly, the 5' portion of transcript after cleavage remained associated with the template in a functional, polyadenylation-competent complex. Efficient cleavage required 5' capping by the human capping enzyme, but the reduction of cleavage seen of transcripts in COOH-terminal domain-less polymerase elongation complexes, was not because of lack of capping.

MLN944 is a novel compound currently being codeveloped by Millennium Pharmaceuticals and Xenova Ltd. as a cancer therapeutic and is in a phase I clinical trial for solid tumors. Although MLN944 was originally proposed to function as a topoisomerase I and II inhibitor, more recent data has shown that it is a DNA-intercalating agent that does not inhibit the catalytic activity of topoisomerase I or II. We show here that MLN944 inhibits incorporation of radiolabeled precursors into RNA preferentially over incorporation into DNA and protein in HCT116 and H460 cells. To determine if MLN944 inhibits transcription, a human RNA polymerase II in vitro transcription system was used. MLN944 inhibited initiation when added before or after the formation of preinitiation complexes and inhibited elongation at higher concentrations. The preferential inhibition of initiation differentiates MLN944 from actinomycin D, which more strongly inhibits elongation. Transcription of all RNA polymerases was inhibited in nuclei isolated from HeLa cells treated with low concentrations of MLN944. Our data are consistent with transcription as the target of the potent cytotoxic effects of MLN944.

Positive transcription elongation factor b (P-TEFb) controls the fraction of initiated RNA polymerase II molecules that make full length transcripts. This important factor is a heterodimer of cyclin-dependent kinase 9 (Cdk9) and one of four cyclin partners, cyclin T1, T2a, T2b or K. There are two isoforms of Cdk9 in mammalian cells, Cdk9(42) and Cdk9(55). Cdk9(55) has a 117 residue amino terminal extension not present in Cdk9(42). An expression vector with a tetracycline-responsive promoter driving FLAG-tagged Cdk9(55) and a HeLa 37 Tet-Off cell line were constructed. FLAG-tagged Cdk9(55) was inducibly expressed and was found to be localized to the nucleus by immunofluorescence. Western analysis of murine tissues showed that the relative abundance of the two forms of Cdk9 varied across different tissues with liver having more Cdk9(55) than Cdk9(42). During adaptation of primary rat hepatocytes to culture the ratio of the two forms of Cdk9 changed. Initially, Cdk9(55) was the predominate form, but as the cells began to enter the cell cycle Cdk9(42) became the major form. During this change, expression of Cdk9(42) was induced, while Cdk9(55) remained relatively constant.

The kinase activity of positive transcription elongation factor b (P-TEFb), composed of cyclin-dependent kinase 9 and cyclin T1 or T2, is required for the transition of RNA polymerase II into productive elongation. P-TEFb activity has been shown to be negatively regulated by association with the small nuclear RNA 7SK and the HEXIM1 protein. Here, we characterize HEXIM2, a previously predicted protein with sequence similarity to HEXIM1. HEXIM2 is expressed in HeLa and Jurkat cells, and glycerol gradient analysis and immunoprecipitations indicate that HEXIM2, like HEXIM1, has a regulated association with P-TEFb. As HEXIM1 is knocked down, HEXIM2 functionally compensates for its association with P-TEFb. Electrophoretic mobility shift assays and in vitro kinase assays demonstrate that HEXIM2 forms complexes containing 7SK and P-TEFb and, in conjunction with 7SK, inhibits P-TEFb kinase activity. Our results provide strong evidence that HEXIM2 is a regulator of P-TEFb function. Furthermore, our results support the idea that the utilization of HEXIM1 or HEXIM2 to bind and inhibit P-TEFb can be differentially regulated in vivo.

Gretchen Schafft, From Racism to Genocide: Anthropology in the Third Reich. Urbana: University of Illinois Press, 2004, 297 pp. While an undeniably disturbing work, From Racism to Genocide is one of the more important books on the history of anthropology to be published in the last three decades. The importance of Gretchen Schafft's book can perhaps best be measured by considering the enormous weight of uncomfortably uncontested silence surrounding scholarly considerations of the uses and meanings of German anthropology under the Nazis. The significance of this silence becomes apparent upon consideration of what Schafft accomplishes in this vital book. Schafft not only breaks this silence using unsettling and rich documentation; but she provides nuanced interpretations and ethical critiques of these anthropological misapplications. While other scholars have written about German anthropology under the Nazis, none of these previous works approach either the level of documentation, depth of study, or the strength of interpretive analysis offered by Schafft. For years Schafft painstakingly gathered and evaluated an astounding amount of German, Polish and American archival materials pertaining to the development and uses of anthropology during the Third Reich, but the genius of this book is found in Schafft's synthetic analysis of the ways that German anthropologists accommodated their science to the needs of the Nazi state. Schafft accomplishes several remarkable feats-any one of these would have been a worthy scholarly accomplishment, but to achieve all of these is singularly remarkable. First, she documents how German anthropological racial "science" informed Nazi political views. Second, Schafft clarifies how Nazi anthropologists helped make the "German Reich a rational, unified, homogenous state with the most optimal gene pool that science could provide" (247). Third, she chronicles how German anthropologists learned to shape and self-censor their scientific findings to better fit the needs of the total Nazi state. Fourth, she shows how medical doctors trained by anthropologists in "racial hygiene" and anthropology at the Kaiser Wilhelm Institute for Anthropology, Human Genetics and Eugenics (KWIA) participated in sterilization and genocidal "euthanasia" campaigns. Finally, Schafft establishes that German anthropologists knew their work was facilitating horrendous human experiments and campaigns of deportation and genocide. The most famous Nazi formally trained in anthropology was Josef Mengele, but Hitler's notions of race and racial purity were also initially informed by his reading of German anthropological racial theories. Most anthropologists' contributions to Nazi efforts were of the small, complacent variety. Some anthropologists served as Nazi bureaucratic functionaries enabling rather than challenging the Nazi's insidious racial laws, working at places like the Anthropological Institute of Vienna where their reputations added legitimacy to the practice of validating racial heredity certificates in compliance with Nazi policies. The Nazis were able to narrow the range of views in German academies by intimidating and firing anthropologists who challenged party doctrine. Eugen Fischer was interrogated by the SS Office of Population and Genetic Health, and was told to expect an early retirement if he continued his research on the positive outcomes of "racial mixing." Fischer complied (though Schafft notes many of his views were already aligned with Nazi ideology) and he became a leader in Nazi academia. Schafft found that, "both a carrot and a stick were held out to anthropologists in the Third Reich. Hitler was talking their language in many instances, although the establishment anthropologists had been more careful in mincing their words" (71). …

Purpose Selective internal radiation therapy (SIRT) with SIR-Spheres® is a new technique for selectively targeting high doses of radiation to tumours within the liver. The primary objectives of this randomised trial were to compare the response rate, time to progressive disease (PD), and toxicity of a regimen of systemic fluorouracil/leucovorin chemotherapy versus the same chemotherapy plus a single administration of SIR-Spheres in patients with advanced colorectal liver metastases. The trial was designed to presage a larger trial that would have survival as the primary outcome. Patients and Methods Twenty-one patients with previously untreated advanced colorectal liver metastases, with or without extrahepatic metastases, were randomised into the study. Results Using RECIST criteria, the response rate for 11 patients receiving the combination treatment was significantly greater than for 10 patients receiving chemotherapy alone (First Integrated Response; 10 PR, 1 SD vs. 0 PR, 6 SD, 4 PD, P

The positive transcription elongation factor b (P-TEFb) plays a pivotal role in productive elongation of nascent RNA molecules by RNA polymerase II. Core active P-TEFb is composed of CDK9 and cyclin T. In addition, mammalian cell extracts contain an inactive P-TEFb complex composed of four components, CDK9, cyclin T, the 7SK snRNA and the MAQ1/HEXIM1 protein. We now report an in vitro reconstitution of 7SK-dependent HEXIM1 association to purified P-TEFb and subsequent CDK9 inhibition. Yeast three-hybrid tests and gel-shift assays indicated that HEXIM1 binds 7SK snRNA directly and a 7SK snRNA-recognition motif was identified in the central part of HEXIM1 (amino acids (aa) 152–155). Data from yeast two-hybrid and pull-down assay on GST fusion proteins converge to a direct binding of P-TEFb to the HEXIM1 C-terminal domain (aa 181–359). Consistently, point mutations in an evolutionarily conserved motif (aa 202–205) were found to suppress P-TEFb binding and inhibition without affecting 7SK recognition. We propose that the RNA-binding domain of HEXIM1 mediates its association with 7SK and that P-TEFb then enters the complex through association with HEXIM1.

All nuclear transcription is interrupted during mitosis. We examined the role of human TTF2, an RNA polymerase (Pol) I and II termination factor, in mitotic repression of transcription elongation. We find that TTF2 levels rise in the cytoplasm in S and G2 and at the onset of mitosis TTF2 translocates into the nucleus. Consistent with a role in termination of all transcription, TTF2 is the only ATP-dependent termination activity associated with Pol II transcription elongation complexes, is largely unaffected by template position, and is impervious to the phosphorylation state of the polymerase. Cells in which TTF2 levels are knocked down showed dramatic retention of Ser2 phosphorylated Pol II on mitotic chromosomes and an increase in chromosome segregation defects.

Economic and academic support for American anthropologists during the Cold War is examined in light of what is known about military and intelligence interests during this period. Some of the questions asked and regions studied by anthropologists were shaped by the limited availability of Area Center funds, public and private foundations’ grants, development projects, and other funding opportunities. The CIA’s covert involvement in the Human Ecology Fund, and the Cold War backdrop of the Modjokuto Project are examined to highlight America’s covert-hegemonic influence on the developement of midcentury anthropology.

This paper examines the public and private context of Morris Opler's Cold War criticism that Betty Meggers's and Leslie White's theoretical perspective was laden with the ideas of crypto-Marxism. While White was significantly influenced by the Marxist tradition, Opler's attacks went beyond the establishment of epistemological influences and entered the realm of McCarthyistic Red baiting. The climate of McCarthyism gave Opler the opportunity to strengthen his criticisms of Meggers's and White's attacks on psychological anthropology with a powerful political threat by linking their work with Stalinism and Marxism. The history of White and Opler's relationship, and the correspondence of Meggers, Opler, White, and others indicate Opler's criticisms were influenced by long-standing personal and professional quarrels with White.

"The idea of measuring the progress of millions of individual students by subjecting them to standardized tests is absurd. This does not measure the progress made by the student; it measures the progress made by the system. Our schools are really factories of mass production where the object isn't to educate and inform, but to produce a homogenous culture of non-thinking conformists and consumers. The finished product is like a fast food hamburger from McDonald's. It's uniformly the same no matter where you buy it from." -Charles Sullivan The Roots of A More Activist Anthropology During the last century anthropological research challenged racial, gender, ethnic, and class discrimination in American society. Among anthropology's most significant activist contributions to 20th century American public policy are its arguments against uniformist visions linking race and ethnicity with intelligence. Given anthropology's past role in challenging the determinative applications of standardized I.Q., it is surprising to find most anthropologists sitting on the sidelines as America prepares for a standardized testing revival-a revival whose outcome stands to be as discriminatory and punitive as the I.Q.-linked immigration or placement schemes of the past century.1 In the early 1900s anthropologists like Franz Boas criticized the biased nature of intelligence tests, and challenged the uses of standardized test results by educational, immigration and law enforcement officials (see Boas 1912 & Wax 2000). Otto Klineberg's critiques of biased I.Q. tests established the social dangers of assigning significant meaning to tests that measured cultural participation more than they measured "innate intelligence" (Klineberg 1935 & 1963). Gene Weltfish suffered the ire of Senator Joseph McCarthy for publishing The Races of Mankind (co-authored with Ruth Benedict) and claiming that "Northern Negroes" had higher I.Q. scores than "Southern Whites" (Price 2004).2 A host of popular anthropologists such as Ashley Montagu, Margaret Mead and Marvin Harris wrote popular articles, essays and books to educate the general public on the dangers of relying on standardized I.Q. tests to sort individuals in any meaningful way. And anthropological critiques of Richard Herrnstein and Charles Murray's 1996 best-seller, The Bell Curve, clarified how economic and social stratification continues to overlay measurements of intelligence and other realms of competency (i.e., Alland 1996; Brace 1996). At the heart of anthropological critiques of I.Q. tests is the observation that these tests do not objectively measure some quantity of "intelligence;" instead these measures are themselves biased tools used to justify the maintenance or creation of systems of stratification. Measurements of human mental capacities are seldom "just measurements," they are themselves social statements: statements of power, desire, hierarchy and ultimately statements of control. These measurements transpire within preexisting political economies and their use tends to reify rather than challenge extant hierarchies. Methodological critiques of standardized tests have historically been met with vicious renunciations by social conservatives. Anthropologists, psychologists and sociologists critiquing the use of culturally-biased tests to sort conscripts during the First World War were attacked as unpatriotic dupes, while critics of racist abuses of IQ tests were frequently labeled "Communists" in the mid-twentieth century (Herman 1995; Price 2004). Today neoconservatives similarly dismiss those who oppose standardized testing regimes as being welfare-state-devotees fearing the loss of their dependent constituencies once they get hooked on phonics and shake their dependency on government cheese.3 But while such reactionary grousing strikes a cord with some Americans, the tilted logic supporting the drive for excessive high stakes testing should be critiqued Current commitments to improving educational standards through an increased reliance on high stakes standardized tests are historically linked to American social engineers' attraction to standardized I. …

A US federal law prohibiting the provision of “material support” or resources to terrorist groups has broad implications for anthropologists and other academics working with groups who may be designated as terrorists and the populations that support them or live under their influence. The broad scope and vague language of the law raises the possibility that individuals engaging in some forms of humanitarian aid, charitable giving, peace-building or academic activities could be prosecuted for offering material aid to terrorists. Problems with the material support law are critically examined as are the dangers faced by anthropologists whose ordinary research, writing and speaking activities might be seen as violating the law. Historical context and the chilling effect on anthropological research and analysis are considered.

L'histoire des relations entre l'anthropologie et les services secrets, pendant ou apres la Guerre froide, est complexe, et des distinctions peuvent etre faites entre des collaborations consenties ou non, directes ou indirectes. L'A. discute plusieurs modalites de ces relations, centrant son propos plus particulierement sur l'histoire de l'anthropologie americaine, evoquant notamment le role de la CIA (ou d'autres agences gouvernementales) et le cas de Ruth Benedict, ou les tentatives d'approches de Vera Rubin par le FBI. En conclusion, il propose quelques reflexions sur la necessite d'une prise en compte et d'une evaluation de ce passe anthropologique, plus particulierement dans le contexte contemporain des sollicitations de collaboration pour la guerre contre le terrorisme.

The well established links between anthropologists and colonialism documented in the work of scholars like Talal Asad, Kathleen Gough, Dell Hymes, Adam Kuper and George Stocking stand in marked contrast with the sparse analysis of anthropological contributions to the wars of the 20th century. The latter reflects certain professional concerns of ethics, historically inevitable blind spots associated with the analysis of recent events, and the problems arising from critical evaluation of the actions of living and recently deceased anthropological elders. While some anthropologists and historians have discussed various aspects of anthropological contributions to warfare, these periodic examinations tend to focus more on the specifics of particular military or intelligence campaigns, while the larger issues embedded in anthropological contributions to warfare are often downplayed. 1 But downplayed or not, these contributions raise serious questions concerning the ethical implications of using cultural knowledge and anthropological knowledge in the waging of war, and reveal fundamental symbiotic links between scholars and state. Twentieth-century anthropologists

The term "RNA editing" was first coined more than a decade ago to describe the phenomenon of uridine insertion into trypanosomatid mitochondrial transcripts. Unlike mRNAs, transcripts of tRNA and rRNA genes are themselves converted into the functional entities they encode. RNA editing events represent additional steps in posttranscriptional processing and, like nucleoside modifications, they may occur at different stages in the pathway. To quantify RNA editing one usually compares the intensity of the bands on a sequencing (or primer extension) ladder that correspond to the edited and unedited versions of the RNA. The first example of tRNA editing in a mitochondrial (mt) system is that reported to occur in the ameboid protozoon Acantbamoeba castellanii. The observed nucleotide substitutions consisted of both purine-to-purine and pyrimidine- to-purine changes, suggesting a mechanism involving base or nucleotide replacement. More recently, it has been shown that nascent mRNAs present in stalled RNA polymerase complexes are substrates for editing by both cytidine and dinucleotide insertion. In a particular study the isolated RNAs were found to be edited to within 14 to 22 nucleotides of the stalled polymerase, suggesting that the insertional editing activity in Physarum is able to act quite close to the site of RNA synthesis. The most recently described mode of tRNA editing is that found in the mitochondria of metazoa.

Developing anti-viral therapies targeting HIV-1 transcription has been hampered by the limited structural knowledge of the proteins involved. HIV-1 hijacks the cellular machinery that controls RNA polymerase II elongation through an interaction of HIV-1 Tat with the positive transcription elongation factor P-TEFb, which interacts with an AF4 family member (AFF1/2/3/4) in the super elongation complex (SEC). Because inclusion of Tat•P-TEFb into the SEC is critical for HIV transcription, we have determined the crystal structure of the Tat•AFF4•P-TEFb complex containing HIV-1 Tat (residues 1-48), human Cyclin T1 (1-266), human Cdk9 (7-332), and human AFF4 (27-69). Tat binding to AFF4•P-TEFb causes concerted structural changes in AFF4 via a shift of helix H5' of Cyclin T1 and the α-3 10 helix of AFF4. The interaction between Tat and AFF4 provides structural constraints that explain tolerated Tat mutations. Analysis of the Tat-binding surface of AFF4 coupled with modeling of all other AF4 family members suggests that AFF1 and AFF4 would be preferred over AFF2 or AFF3 for interaction with Tat•P-TEFb. The structure establishes that the Tat-TAR recognition motif (TRM) in Cyclin T1 interacts with both Tat and AFF4, leading to the exposure of arginine side chains for binding to TAR RNA. Furthermore, modeling of Tat Lys28 acetylation suggests that the acetyl group would be in a favorable position for H-bond formation with Asn257 of TRM, thereby stabilizing the TRM in Cyclin T1, and provides a structural basis for the modulation of TAR RNA binding by acetylation of Tat Lys28.

Gdown1, the substoichiometric 13th subunit of RNA polymerase II (pol II), has an important role in pausing during the initial stage of transcript elongation. However, Gdown1 quantitatively displaces the essential initiation factor TFIIF from free pol II and elongating pol II. Thus, it is not clear how or even if pol II can initiate in the presence of Gdown1. Using an in vitro transcription system with purified factors and pol II lacking Gdown1, we found that although Gdown1 is strongly inhibitory to transcription when prebound to pol II, a fraction of complexes do remain active. Surprisingly, when Gdown1 is added to complete preinitiation complexes (PICs), it does not inhibit initiation or functionally associate with the PICs. Gdown1 does associate with pol II during the early stage of transcript elongation but this association is competitive with TFIIF. By phosphorylating TFIIF, PICs can be assembled that do not retain TFIIF. Gdown1 also fails to functionally associate with these TFIIF-less PICs, but once polymerase enters transcript elongation, complexes lacking TFIIF quantitatively bind Gdown1. Our results provide a partial resolution of the paradox of the competition between Gdown1 and TFIIF for association with pol II. Although Gdown1 completely displaces TFIIF from free pol II and elongation complexes, Gdown1 does not functionally associate with the PIC. Gdown1 can enter the transcription complex immediately after initiation. Modification of TFIIF provides one pathway through which efficient Gdown1 loading can occur early in elongation, allowing downstream pausing to be regulated.

By phosphorylating negative elongation factors and the C-terminal domain of RNA polymerase II (RNAPII), positive transcription elongation factor b (P-TEFb), which is composed of CycT1 or CycT2 and CDK9, activates eukaryotic transcription elongation. In growing cells, it is found in active and inactive forms. In the former, free P-TEFb is a potent transcriptional coactivator. In the latter, it is inhibited by HEXIM1 or HEXIM2 in the 7SK small nuclear ribonucleoprotein (snRNP), which contains, additionally, 7SK snRNA, methyl phosphate-capping enzyme (MePCE), and La-related protein 7 (LARP7). This P-TEFb equilibrium determines the state of growth and proliferation of the cell. In this study, the release of P-TEFb from the 7SK snRNP led to increased synthesis of HEXIM1 but not HEXIM2 in HeLa cells, and this occurred only from an unannotated, proximal promoter. ChIP with sequencing revealed P-TEFb-sensitive poised RNA polymerase II at this proximal but not the previously annotated distal HEXIM1 promoter. Its immediate upstream sequences were fused to luciferase reporters and were found to be responsive to many P-TEFb-releasing compounds. The superelongation complex subunits AF4/FMR2 family member 4 (AFF4) and elongation factor RNA polymerase II 2 (ELL2) were recruited to this proximal promoter after P-TEFb release and were required for its transcriptional effects. Thus, P-TEFb regulates its own equilibrium in cells, most likely to maintain optimal cellular homeostasis.

No abstract is available.

Tat stimulates human immunodeficiency virus, type 1 (HIV-1), transcription elongation by recruitment of the human transcription elongation factor P-TEFb, consisting of CDK9 and cyclin T1, to the TAR RNA structure. It has been demonstrated further that CDK9 phosphorylation is required for high affinity binding of Tat/P-TEFb to the TAR RNA structure and that the state of P-TEFb phosphorylation may regulate Tat transactivation. We now demonstrate that CDK9 phosphorylation is uniquely regulated in the HIV-1 preinitiation and elongation complexes. The presence of TFIIH in the HIV-1 preinitiation complex inhibits CDK9 phosphorylation. As TFIIH is released from the elongation complex between +14 and +36, CDK9 phosphorylation is observed. In contrast to the activity in the "soluble" complex, phosphorylation of CDK9 is increased by the presence of Tat in the transcription complexes. Consistent with these observations, we have demonstrated that purified TFIIH directly inhibits CDK9 autophosphorylation. By using recombinant TFIIH subcomplexes, our results suggest that the XPB subunit of TFIIH is responsible for this inhibition of CDK9 phosphorylation. Interestingly, our results further suggest that the phosphorylated form of CDK9 is the active kinase for RNA polymerase II carboxyl-terminal domain phosphorylation.

Studying the sensitivity of transcription to the nucleotide analog 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole has led to the discovery of a number of proteins involved in the regulation of transcription elongation by RNA polymerase II. We have developed a highly purified elongation control system composed of three purified proteins added back to isolated RNA polymerase II elongation complexes. Two of the proteins, 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole sensitivity-inducing factor (DSIF) and negative elongation factor (NELF), act as negative transcription elongation factors by increasing the time the polymerase spent at pause sites. P-TEFb reverses the negative effect of DSIF and NELF through a mechanism dependent on its kinase activity. TFIIF is a general initiation factor that positively affects elongation by decreasing pausing. We show that TFIIF functionally competes with DSIF and NELF, and this competition is dependent on the relative concentrations of TFIIF and NELF.

Flavopiridol (L86-8275, HMR1275) is a cyclin-dependent kinase (Cdk) inhibitor in clinical trials as a cancer therapy that has been recently shown to block human immunodeficiency virus Tat transactivation and viral replication through inhibition of positive transcription elongation factor b (P-TEFb). Flavopiridol is the most potent P-TEFb inhibitor reported and the first Cdk inhibitor that is not competitive with ATP. We examined the ability of flavopiridol to inhibit P-TEFb (Cdk9/cyclin T1) phosphorylation of both RNA polymerase II and the large subunit of the 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor and found that the IC(50) determined was directly related to the concentration of the enzyme. We concluded that the flavonoid associates with P-TEFb with 1:1 stoichiometry even at concentrations of enzyme in the low nanomolar range. These results indicate that the apparent lack of competition with ATP could be caused by a very tight binding of the drug. We developed a novel immobilized P-TEFb assay and demonstrated that the drug remains bound for minutes even in the presence of high salt. Flavopiridol remained bound in the presence of a 1000-fold excess of the commonly used inhibitor DRB, suggesting that the immobilized P-TEFb could be used in a simple screening assay that would allow the discovery or characterization of compounds with binding properties similar to flavopiridol. Finally, we compared the ability of flavopiridol and DRB to inhibit transcription in vivo using nuclear run-on assays and concluded that P-TEFb is required for transcription of most RNA polymerase II molecules in vivo.

Foerstal, Leonora, and Angela Gilliam, eds. 1992 Confronting the Margaret Mead Legacy: Scholarship, Empire, and the South Pacific. Philadelphia: Temple University Press. Krook, Susan P. 1993 An Analysis of Franz Boas' Achievements and Work Emphasis during the Last Five Years of His Life, Based on Documentation and Interpretation of the Federal Bureau of Investigation File Maintained on Him from 1936 to 1950. Ph.D. dissertation, University of Colorado, Boulder. Leacock, Eleanor 1982 Marxism and Anthropology. In The Left Academy: Marxist Scholarship on American Campuses. Bertell Ollman and Edward Vernoff, eds. Pp. 242-276. New York: McGraw-Hill. Nader, Laura 1997 The Phantom Factor: Impact of the Cold War on Anthropology. In The Cold War and the University: Toward an Intellectual History of the Postwar Years. Noam Chomsky et al. Pp. 107-146. New York: New Press. Peace, William 1993 Leslie White and Evolutionary Theory. Dialectical Anthropology 18:123-151. 1998 Bernhard Stern, Leslie A. White, and an Anthropological Appraisal of the Russian Revolution. American Anthropologist 100:84-93. Peace, William, and David Price N.d. The Cold War and Academics: The Case of Leslie White. Price, David 1997 Cold War Anthropology: Collaborators and Victims of the National Security State. Identities 4:1-42. Schrecker, Ellen W. 1986 No Ivory Tower: McCarthyism and the Universities. New York: Oxford University Press. 1998 Many Are the Crimes: McCarthyism in America. Boston: Little, Brown. White, Leslie A. 1931 An Anthropological Appraisal of the Russian Revolution. The New Masses 6:14-16. White, Leslie A. (aka John Steel) 1932 The Struggle for Food and Freedom. The Weekly People, March 19:3.

In this review essay, the academic merits of three anthropological blogs (“Savage Minds,”“Zero Anthropology”[formerly “Open Anthropology”], and the official blog of the American Anthropological Association) are considered. The review examines differences between group-blog projects (such “Savage Minds”), single-voiced blogs (such as “Zero Anthropology”), and official blogs representing central anthropological institutions (the AAA's blog) and identifies roles and strengths of each of these blog forms.

P-TEFb, a heterodimer of the kinase Cdk9 and cyclin T, was isolated as a factor that stimulates formation of productive transcription elongation complexes in vitro. Here, we show that P-TEFb is located at >200 distinct sites on Drosophila polytene chromosomes. Upon heat shock, P-TEFb, like the regulatory factor HSF, is rapidly recruited to heat shock loci, and this recruitment is blocked in an HSF mutant. Yet, HSF binding to DNA is not sufficient to recruit P-TEFb in vivo, and HSF and P-TEFb immunostainings within a heat shock locus are not coincident. Insight to the function of P-TEFb is offered by experiments showing that the direct recruitment of a Gal4-binding domain P-TEFb hybrid to an hsp70 promoter in Drosophilacells is sufficient to activate transcription in the absence of heat shock. Analyses of point mutants show this P-TEFb stimulation is dependent on Cdk9 kinase activity and on Cdk9's interaction with cyclin T. These results, coupled with the frequent colocalization of P-TEFb and the hypophosphorylated form of RNA polymerase II (Pol II) found at promoter-pause sites, support a model in which P-TEFb acts to stimulate promoter-paused Pol II to enter into productive elongation.

The elongation phase of transcription by RNA polymerase II is one of the many steps during the generation of mature mRNAs that is subject to regulation. Shortly after initiation, RNA polymerase II comes under the control of negative transcription elongation factors, generally termed N-TEFs, and enters abortive elongation (51). During this postinitiation process, only short transcripts are generated that may be prematurely terminated. These short transcripts arise from transcription of many genes, including c-myb, c-myc, c-fos, HSP70, and the human immunodeficiency virus (HIV) long terminal repeat (LTR), and are normally subject to rapid degradation (3, 63). Escape from the action of N-TEF requires the action of at least one positive transcription elongation factor (P-TEF), eventually identified as P-TEFb (52). P-TEFb allows the transition into productive elongation, producing long transcripts from which mRNAs are derived. In this way, the fraction of initiating RNA polymerase II molecules that produce full-length transcripts is controlled by a selection process that occurs early in the elongation phase of the transcription cycle. After the transition is made into productive elongation, the efficiency of elongation may be influenced by additional factors, including S-II, TFIIF, ELL, and elongin (62, 65).