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Supplementary Figures 1-6, Table 1 from FUS/TLS Is a Novel Mediator of Androgen-Dependent Cell-Cycle Progression and Prostate Cancer Growth

A requirement for PKCε in exiting from the Aurora B dependent abscission checkpoint is associated with events at the midbody, however, the recruitment, retention and action of PKCε in this compartment are poorly understood. Here, the prerequisite for 14-3-3 complex assembly in this pathway is directly linked to the phosphorylation of Aurora B S227 at the midbody. However, while essential for PKCε control of Aurora B, 14-3-3 association is shown to be unnecessary for the activity-dependent enrichment of PKCε at the midbody. This localisation is demonstrated to be an autonomous property of the inactive PKCε D532N mutant, consistent with activity-dependent dissociation. The C1A and C1B domains are necessary for this localisation, while the C2 domain and inter-C1 domain (IC1D) are necessary for retention at the midbody. Furthermore, it is shown that while the IC1D mutant retains 14-3-3 complex proficiency, it does not support Aurora B phosphorylation, nor rescues division failure observed with knockdown of endogenous PKCε. It is concluded that the concerted action of multiple independent events facilitates PKCε phosphorylation of Aurora B at the midbody to control exit from the abscission checkpoint.

Guanine rich regions of oligonucleotides fold into quadruple-stranded structures called G-quadruplexes (G4s). Increasing evidence suggests that these G4 structures form in vivo and play a crucial role in cellular processes. However, their direct observation in live cells remains a challenge. Here we demonstrate that a fluorescent probe (DAOTA-M2) in conjunction with fluorescence lifetime imaging microscopy (FLIM) can identify G4s within nuclei of live and fixed cells. We present a FLIM-based cellular assay to study the interaction of non-fluorescent small molecules with G4s and apply it to a wide range of drug candidates. We also demonstrate that DAOTA-M2 can be used to study G4 stability in live cells. Reduction of FancJ and RTEL1 expression in mammalian cells increases the DAOTA-M2 lifetime and therefore suggests an increased number of G4s in these cells, implying that FancJ and RTEL1 play a role in resolving G4 structures in cellulo., Direct observation of G-quadruplexes (G4s) in live cells is challenging. Here the authors report a method to identify G4s within the nuclei of live and fixed cells using a fluorescent probe combined with fluorescence lifetime imaging microscopy.

Chemical probes that covalently modify cysteine residues in a protein‐specific manner are valuable tools for biological investigations. Covalent fragments are increasingly implemented as probe starting points, but the complex relationship between fragment structure and binding kinetics makes covalent fragment optimization uniquely challenging. We describe a new technique in covalent probe discovery that enables data‐driven optimization of covalent fragment potency and selectivity. This platform extends beyond the existing repertoire of methods for identifying covalent fragment hits by facilitating rapid multiparameter kinetic analysis of covalent structure–activity relationships through the simultaneous determination of K i, k inact and intrinsic reactivity. By applying this approach to develop novel probes against electrophile‐sensitive kinases, we showcase the utility of the platform in hit identification and highlight how multiparameter kinetic analysis enabled a successful fragment‐merging strategy., Breaking into fragments: A biophysical platform for determining the complex structure–activity relationships of covalent fragments. By using this approach, a novel series of covalent fragments has been identified for targeting electrophile‐sensitive kinases; optimization is facilitated by covalent fragment merging.

The PKCε-regulated genome protective pathway provides transformed cells a failsafe to successfully complete mitosis. Despite the necessary role for Aurora B in this programme, it is unclear whether its requirement is sufficient or if other PKCε cell cycle targets are involved. To address this, we developed a trapping strategy using UV-photocrosslinkable amino acids encoded in the PKCε kinase domain. The validation of the mRNA binding protein SERBP1 as a PKCε substrate revealed a series of mitotic events controlled by the catalytic form of PKCε. PKCε represses protein translation, altering SERBP1 binding to the 40 S ribosomal subunit and promoting the assembly of ribonucleoprotein granules containing SERBP1, termed M-bodies. Independent of Aurora B, SERBP1 is shown to be necessary for chromosome segregation and successful cell division, correlating with M-body formation. This requirement for SERBP1 demonstrates that Aurora B acts in concert with translational regulation in the PKCε-controlled pathway exerting genome protection., PKCε is known to exert a role in genome protection by directly phosphorylating and switching the specificity of Aurora B. Here the authors identify SERBP1 as a parallel mitotic PKCε substrate controlling translation and ensuring the integrity of chromosome segregation and successful cell division.

Guanine-rich sequences of DNA are known to readily fold into tetra-stranded helical structures known as G-quadruplexes (G4). Due to their biological relevance, G4s are potential anticancer drug targets and therefore there is significant interest in molecules with high affinity for these structures. Most G4 binders are polyaromatic planar compounds which π-π stack on the G4's guanine tetrad. However, many of these compounds are not very selective since they can also intercalate into duplex DNA. Herein we report a new class of binder based on an octahedral cobalt(III) complex that binds to G4 via a different mode involving hydrogen bonding, electrostatic interactions and π-π stacking. We show that this new compound binds selectivity to G4 over duplex DNA (particularly to the G-rich sequence of the c-myc promoter). This new octahedral complex also has the ability to template the formation of G4 DNA from the unfolded sequence. Finally, we show that upon binding to G4, the complex prevents helicase Pif1-p from unfolding the c-myc G4 structure.

Small molecules that react to form covalent bonds with proteins are widely used as biological tools and therapeutic agents. Screening cysteine-reactive fragments against a protein target is an efficient way to identify chemical starting points for covalent probe development. Mass spectrometry is often used to identify the site and degree of covalent fragment binding. However, robust hit identification requires characterization of the kinetics of covalent binding that can be readily achieved using quantitative irreversible tethering. This screening platform uses a non-specific cysteine-reactive fluorogenic probe to monitor the rate of reaction between covalent fragments and cysteine containing biomolecules. Fragment libraries are simultaneously screened against the target protein and glutathione, which functions as a control, to identify hit fragments with kinetic selectivity for covalent modification of the target. Screening by quantitative irreversible tethering accounts for variations in the intrinsic reactivity of individual fragments enabling robust hit identification and ranking.

RNA viruses are critically dependent upon virally encoded proteases that cleave the viral polyproteins into functional mature proteins. Many of these proteases are structurally conserved with an essential catalytic cysteine and this offers the opportunity to irreversibly inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that selectively target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we effectively re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold as well as similar catalytic-triad. We demonstrate that the hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity. In addition, we provide the first demonstration that targeting the active site cysteine of Mpro can also have profound allosteric effects, distorting secondary structures required for formation of the active dimeric unit of Mpro. These new data provide novel mechanistic insights into the design of EV71 3Cpro and SARS-CoV-2 Mpro inhibitors and identify acrylamide-tagged pharmacophores for elaboration into more selective agents of therapeutic potential.

Objective The purpose of this report is to describe a patient with scapholunate advanced collapse (SLAC) of the wrist. Clinical Features A 38-year-old man presented to a chiropractic teaching clinic with right wrist pain after falling off of the tailgate of a truck 7 years prior. The mechanism of injury was a fall on an outstretched hand. Ultrasonography and radiography were performed, which demonstrated abnormal lunate kinematics and scapholunate interval diastasis associated with a clenched-fist maneuver. These findings were consistent with SLAC. Intervention and Outcome Following the diagnosis of SLAC, the wrist was splinted. Conservative care consisting of physical therapy included paraffin dips, therapeutic ultrasound, and stretching. The patient received only minimal alleviation of pain, and a surgical consultation was obtained. The patient elected surgical intervention, utilizing the proximal row carpectomy procedure. Conclusion This case demonstrates a patient with chronic wrist pain, with progression to carpal instability, which ultimately manifested as SLAC. We demonstrate, utilizing multiple imaging modalities, both preoperative and postoperative findings. To our knowledge, this is the first case to describe the use of diagnostic ultrasonography in the evaluation of the proximal row carpectomy procedure.

Guanine-rich sequences of DNA are known to readily fold into tetra-stranded helical structures known as G-quadruplexes (G4). Due to their biological relevance, G4s are potential anticancer drug targets and therefore there is significant interest in molecules with high affinity for these structures. Most G4 binders are polyaromatic planar compounds which π-π stack on the G4's guanine tetrad. However, many of these compounds are not very selective since they can also intercalate into duplex DNA. Herein we report a new class of binder based on an octahedral cobalt(III) complex that binds to G4 via a different mode involving hydrogen bonding, electrostatic interactions and π-π stacking. We show that this new compound binds selectivity to G4 over duplex DNA (particularly to the G-rich sequence of the c-myc promoter). This new octahedral complex also has the ability to template the formation of G4 DNA from the unfolded sequence. Finally, we show that upon binding to G4, the complex prevents helicase Pif1-p from unfolding the c-myc G4 structure.

Multiple myeloma (MM) is characterized by over-expression of cyclin D1 (CCND1) or D2 (CCND2), which control G1 phase cell-cycle progression. Proteolytic degradation of CCND1 (but not CCND2), resulting in G1 arrest, is reported in non-MM cells post-DNA damage, affecting DNA repair and survival. We examined the effect of ionizing radiation (IR) on D-cyclin levels and cell-cycle kinetics of MM cells, exploring differences based on D-cyclin expression. We showed that CCND1 is downregulated, whereas CCND2 is not, following IR. This did not lead to hypo-phosphorylation of retinoblastoma protein or G1 arrest. Both CCND1- and CCND2-expressing MM cells arrested in S/G2/M, and did not differ in other cell-cycle proteins or sensitivity to IR. When treated with a CDK4/6 inhibitor, both CCND1 and CCND2 MM cells arrested in G1 and therefore are subject to physiological regulation at this checkpoint. Immunoprecipitation showed that, despite CCND1 degradation following IR, sufficient protein remains bound to CDK4/6 to prevent G1 arrest. Aberrant expression of CCND1 driven from the IGH promoter in t(11;14) MM cells maintains progression through G1 to arrest in S/G2/M. Differential expression of D-cyclin does not appear to affect cell-cycle response to IR, and is unlikely to underlie differential sensitivity to DNA damage.

Vinyl sulfonamides are valuable electrophiles for targeted protein modification and inhibition. We describe a novel approach to the synthesis of terminal vinyl sulfonamides which uses mild oxidative conditions to induce elimination of an α-selenoether masking group. The method complements traditional synthetic approaches and typically yields vinyl sulfonamides in high purity after aqueous work-up without requiring column chromatography of the final electrophilic product. The methodology is applied to the synthesis of covalent fragments for use in irreversible protein tethering and crucially enables the attachment of diverse fragments to the vinyl sulfonamide warhead via a chemical linker. Using thymidylate synthase as a model system, ethylene glycol is identified as an effective linker for irreversible protein tethering.

Vinyl sulfonamides are valuable electrophiles for targeted protein modification and inhibition. We describe a novel approach to the synthesis of terminal vinyl sulfonamides which uses mild oxidative conditions to induce elimination of an α-selenoether masking group. The method complements traditional synthetic approaches and typically yields vinyl sulfonamides in high purity after aqueous work-up without requiring column chromatography of the final electrophilic product. The methodology is applied to the synthesis of covalent fragments for use in irreversible protein tethering and crucially enables the attachment of diverse fragments to the vinyl sulfonamide warhead via a chemical linker. Using thymidylate synthase as a model system, ethylene glycol is identified as an effective linker for irreversible protein tethering.

Objective The aim of this case report is to describe the response of a patient with chronic pain who received chiropractic care in a federally qualified health center. Clinical Features A 61-year-old female patient with neck and back pain after a traumatic motor vehicle accident 3 years prior was referred for chiropractic care. She had neck pain, low back pain, knee pain, and pain associated with over 20 surgeries, as well as depression, opioid dependence, and low quality of life. Interventions and Outcomes The patient was treated with chiropractic manipulation for her low back and neck pain and was counseled on nutrition and exercise. After 6 months, she reported improvements in pain, improved quality of life, and discontinuation of opioid pain medication. Conclusion This patient improved after a course of chiropractic care that was integrated into a federally qualified health center.

Cysteine -­ reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high -­ quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan -­ reactive compounds. Here we describe quantitative irreversible tethering (qIT) , a general method for screening cysteine -­ reactive small molecules based upon the maximization of kinetic selectivity. We apply this method prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and g uide further optimization. The power of this technique is highlighted by the identification of a Cdk2 -­ selective allosteric (type IV) kinase inhibitor whose novel mode -­ of -­ action could be exploited therapeutically.

The genus Theileria includes tick-transmitted apicomplexan parasites of ruminants with substantial economic impact in endemic countries. Some species, including Theileria parva and Theileria annulata, infect leukocytes where they induce phenotypes that are shared with some cancers, most notably immortalization, hyperproliferation, and dissemination. Despite considerable research into the affected host signaling pathways, the parasite proteins directly responsible for these host phenotypes remain unknown. In this review we outline current knowledge on the manipulation of host cells by transformation-inducing Theileria, and we propose that comparisons between cancer biology and host-Theileria interactions can reveal chemotherapeutic targets against Theileria-induced pathogenesis based on cancer treatment approaches.

Cysteine‐reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high‐quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan‐reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine‐reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2‐selective allosteric (type IV) kinase inhibitor whose novel mode‐of‐action could be exploited therapeutically.

During meiosis, reciprocal exchange between homologous chromosomes occurs as a result of crossovers (COs). CO frequency varies within genomes and is subject to genetic, epigenetic and environmental control. As robust measurement of COs is limited by their low numbers, typically 1-2 per chromosome, we adapted flow cytometry for use with Arabidopsis transgenic fluorescent protein-tagged lines (FTLs) that express eCFP, dsRed or eYFP fluorescent proteins in pollen. Segregation of genetically linked transgenes encoding fluorescent proteins of distinct colors can be used to detect COs. The fluorescence of up to 80,000 pollen grains per individual plant can be measured in 10-15 min using this protocol. A key element of CO control is interference, which inhibits closely spaced COs. We describe a three-color assay for the measurement of CO frequency in adjacent intervals and calculation of CO interference. We show that this protocol can be used to detect changes in CO frequency and interference in the fancm zip4 double mutant. By enabling high-throughput measurement of CO frequency and interference, these methods will facilitate genetic dissection of meiotic recombination control.

We hereby present a simple yet novel chemical synthesis of a family of γ-modified ATPs bearing functional groups on the γ-phosphate that are amenable to further derivatization by highly selective chemical manipulations (e.g., click chemistry, Staudinger ligations). A preliminary screen of these compounds as phosphate donors with a typical wild type protein kinase (cdk2) and one of its known substrates p27kip1 is also presented. © 2009 Elsevier Ltd. All rights reserved.

Over the last few decades, it has become apparent that oncogenic proliferative signals are coupled to a variety of growth inhibitory responses, such as the induction of apoptotic cell death or irreversible cell cycle arrest known as 'cellular senescence'. Thus, both apoptosis and cellular senescence are thought to act as important tumor suppression mechanisms. Unlike apoptotic cells, however, senescent cells remain viable for long periods of time and accumulate with increasing age in various organs and tissues. Moreover, recent studies reveal that although cellular senescence initially functions as a tumor suppressive process, it may eventually exhibit tumor-promoting effects. Therefore, it is conceivable that accumulation of senescent cells during the ageing process in vivo may contribute to the age-related increase in cancer incidence. In this review, we provide an update and perspective on recent advances made in understanding the deleterious side effects of cellular senescence.

Progression of prostate cancer is highly dependent upon the androgen receptor pathway, such that knowledge of androgen-regulated proteins is vital to understand and combat this disease. Using a proteomic screen, we found the RNA-binding protein FUS/TLS (Fused in Ewing's Sarcoma/Translocated in Liposarcoma) to be downregulated in response to androgen. FUS has recently been shown to be recruited by noncoding RNAs to the regulatory regions of target genes such as cyclin D1, in which it represses transcription by disrupting complex formation. Here we show that FUS has some characteristics of a putative tumor suppressor, as its overexpression promoted growth inhibition and apoptosis of prostate cancer cells, whereas its knockdown increased cell proliferation. This effect was reproducible in vivo, such that increasing FUS levels in tumor xenografts led to dramatic tumor regression. Furthermore, FUS promoted conditions that favored cell-cycle arrest by reducing the levels of proliferative factors such as cyclin D1 and Cdk6 and by increasing levels of the antiproliferative Cdk inhibitor p27. Immunohistochemical analysis revealed that FUS expression is inversely correlated with Gleason grade, demonstrating that patients with high levels of FUS survived longer and were less likely to have bone metastases, suggesting that loss of FUS expression may contribute to cancer progression. Taken together, our results address the question of how androgens regulate cell-cycle progression, by demonstrating that FUS is a key link between androgen receptor signaling and cell-cycle progression in prostate cancer. Cancer Res; 71(3); 914–24. ©2010 AACR.

Several mammalian forkhead transcription factors have been shown to impact on cell cycle regulation and are themselves linked to cell cycle control systems. Here we have investigated the little studied mammalian forkhead transcription factor FOXK2 and demonstrate that it is subject to control by cell cycle-regulated protein kinases. FOXK2 exhibits a periodic rise in its phosphorylation levels during the cell cycle, with hyperphosphorylation occurring in mitotic cells. Hyperphosphorylation occurs in a cyclin-dependent kinase (CDK)·cyclin-dependent manner with CDK1·cyclin B as the major kinase complex, although CDK2 and cyclin A also appear to be important. We have mapped two CDK phosphorylation sites, serines 368 and 423, which play a role in defining FOXK2 function through regulating its stability and its activity as a transcriptional repressor protein. These two CDK sites appear vital for FOXK2 function because expression of a mutant lacking these sites cannot be tolerated and causes apoptosis.

Cyclin-dependent kinase 2 (cdk2) is a central regulator of the mammalian cell cycle. Here we describe the properties of a mutant form of cdk2 identified during large-scale sequencing of protein kinases from cancerous tissue. The mutation substituted a leucine for a proline in the PSTAIRE helix, the central motif in the interaction of the cdk with its regulatory cyclin subunit. We demonstrate that whilst the mutant cdk2 is considerably impaired in stable cyclin association, it is still able to generate an active kinase that can functionally complement defective cdks in vivo. Molecular dynamic simulations and biophysical measurements indicate that the observed biochemical properties likely stem from increased flexibility within the cyclin-binding helix.

Explicit solvent ab initio molecular dynamics simulations have been used to study the activation of the nitrogen mustards mechlorethamine and phosphoramide mustard into the aziridinium ion intermediates known to be involved in the alkylation of DNA. The simulations predict a concerted reaction occurring by way of neighboring-group participation with the nearby nucleophilic tertiary nitrogen, in agreement with previous theoretical studies. The calculated activation free energy of 20.4 kcal/mol for mechlorethamine agrees well with the value of 22.5 kcal/mol determined from available experimental data. Furthermore, these simulations indicate a dynamic transition state characterized by pronounced changes in the local water structure within the first hydration shell. Trajectories initiated from the transition-state region toward products reveal a reaction that proceeds directly to the solvent-separated ion pair. Failure to cross the transition state was observed in a small number of trajectories where the degree of coordination with the leaving group is less favorable for reaction. Direct vibrational excitation of mechlorethamine alone is not sufficient to induce reaction, even with energies far in excess of the activation energy. The simulations suggest that reactivity is strongly dependent on the degree of coordination and orientation of water molecules within the vicinity of the leaving group. The complete mechanism involving solvent reorganization, ionization of the C-Cl bond, and internal cyclization of the aziridinium ion ring was captured from elevated temperature simulations. Rate constants for aziridinium ion ring formation from both mechlorethamine and phosphoramide mustard (the alkylating moiety of cyclophosphamide) are calculated and compared with available pharmacokinetic data.

N-myristoylation is the attachment of a 14-carbon fatty acid, myristate, onto the N-terminal glycine residue of target proteins, catalysed by N-myristoyltransferase (NMT), a ubiquitous and essential enzyme in eukaryotes. Many of the target proteins of NMT are crucial components of signalling pathways, and myristoylation typically promotes membrane binding that is essential for proper protein localisation or biological function. NMT is a validated therapeutic target in opportunistic infections of humans by fungi or parasitic protozoa. Additionally, NMT is implicated in carcinogenesis, particularly colon cancer, where there is evidence for its upregulation in the early stages of tumour formation. However, the study of myristoylation in all organisms has until recently been hindered by a lack of techniques for detection and identification of myristoylated proteins. Here we introduce the chemistry and biology of N-myristoylation and NMT, and discuss new developments in chemical proteomic technologies that are meeting the challenge of studying this important co-translational modification in living systems.

The protein kinase superfamily is one of the most important families of enzymes in molecular biology. Protein kinases typically catalyze the transfer of the -phosphate from ATP to a protein substrate (a highly ubiquitous cellular reaction), thereby controlling key areas of cell regulation. Deregulation of protein kinases is known to contribute to many human diseases, and selective inhibitors of protein kinases are a major area of interest in medicinal chemistry. However, a detailed understanding of many kinase pathways is currently lacking. Before we can effectively design medicinally relevant selective kinase inhibitors, it is necessary to understand the role played by a given kinase in specific signal-transduction cascades and to decipher its protein targets. Here, we describe recent advances towards dissecting protein kinase function through the use of chemical genetics. © 2009 Future Science Ltd.

Expression of the p16Ink4a tumor suppressor gene, a sensor of oncogenic stress, is up-regulated by a variety of potentially oncogenic stimuli in cultured primary cells. However, because p16Ink4a expression is also induced by tissue culture stress, physiological mechanisms regulating p16Ink4a expression remain unclear. To eliminate any potential problems arising from tissue culture–imposed stress, we used bioluminescence imaging for noninvasive and real-time analysis of p16Ink4a expression under various physiological conditions in living mice. In this study, we show that oncogenic insults such as ras activation provoke epigenetic derepression of p16Ink4a expression through reduction of DNMT1 (DNA methyl transferase 1) levels as a DNA damage response in vivo. This pathway is accelerated in the absence of p53, indicating that p53 normally holds the p16Ink4a response in check. These results unveil a backup tumor suppressor role for p16Ink4a in the event of p53 inactivation, expanding our understanding of how p16Ink4a expression is regulated in vivo.

Four enantiopure cytisine-inspired scaffolds can be accessed via a versatile pyrrolidine template derived from a stereocontrolled [3+2] azomethine ylide-alkene cycloaddition. Differential ester protection allows for the selective formation of either a bridged bicyclic or tricyclic scaffold via pyridone cyclization. Solid-phase diversification of the pyridone scaffolds yielded a diverse library of 15,000 compounds enabling the discovery of a novel class of Bcl-2 inhibitors.

In normal tissue, cell division is carefully regulated to maintain the correct proliferative balance. Abnormal cell division underlies many hypoproliferative and hyperproliferative disorders, including cancer, and a better understanding of the mechanisms involved could lead to new strategies for treatment and prevention. Cellular senescence, a state of irreversible growth arrest, was first described as a limit to the replicative life span of somatic cells after serial cultivation in vitro. Recently, however, it has also been shown to be triggered prematurely by potentially oncogenic stimuli such as oncogene expression, oxidative stress, and DNA damage in cell culture studies. These data suggest that cellular senescence is therefore acting as a tumor-protective fail-safe mechanism. However, the significance of cellular senescence has remained an issue of debate over the years, with the possibility that it might be a cell culture-related artifact. Recent reports on oncogene-induced senescence detected in premalignant tumors have provided evidence to validate its role as a physiological response to prevent oncogenesis in vivo. In this review, we discuss the mechanisms for cellular senescence and its roles in vivo.

In addition to the well characterized phosphoinositide second messengers derived from the plasma membrane, increasing evidence supports the existence of a nuclear phosphoinositide signaling network. The aim of this investigation was to dissect the role played by nuclear phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) in cell cycle progression and to determine the cell cycle regulatory component(s) that are involved. A number of cytosolic/nuclear PtdIns(4,5)P2-deficient Swiss 3T3 cell lines were established, and their G 0/G 1/S cell cycle phase transitions induced by defined mitogens were examined. Our results demonstrate that nuclear PtdIns(4,5)P2 down-regulation caused a delay in phorbol ester-induced S phase entry and that this was at least in part channeled through cyclin A2 at the transcriptional level. In summary, these data identify cyclin A2 as a downstream effector of the nuclear PtdIns(4,5)P2 signaling network and highlight the importance of nuclear PtdIns(4,5)P2 in the regulation of mammalian mitogenesis.

Members of the γ2-herpesvirus family encode cyclin-like proteins that have the ability to deregulate mammalian cell cycle control. Here we report the key features of the viral cyclin encoded by Murine Herpesvirus 68, M cyclin. M cyclin preferentially associated with and activated cdk2; the M cyclin/cdk2 holoenzyme displayed a strong reliance on phosphorylation of the cdk T loop for activity. cdk2 associated with M cyclin exhibited substantial resistance to the cdk inhibitor proteins p21 Cip and p27 Kip . Furthermore, M cyclin directed cdk2 to phosphorylate p27 Kip1 on threonine 187 (T187) and cellular expression of M cyclin led to down-regulation of p27 Kip1 and the partial subversion of the associated G1 arrest. Mutation of T187 to a non-phosphorylatable alanine rendered the p27 Kip1 -imposed G1 arrest resistant to M cyclin expression. Unlike the related K cyclin, M cyclin was unable to circumvent the G1 arrest associated with p21 Cip1 and was unable to direct its associated catalytic subunit to phosphorylate this cdk inhibitor. These results imply that M cyclin has properties that are distinct from other viral cyclins and that M cyclin expression alone is insufficient for S phase entry.

Although the role of p21 Waf1/Cip1 gene expression is well documented in various cell culture studies, its in vivo roles are poorly understood. To gain further insight into the role of p21 Waf1/Cip1 gene expression in vivo , we attempted to visualize the dynamics of p21 Waf1/Cip1 gene expression in living animals. In this study, we established a transgenic mice line (p21- p -luc) expressing the firefly luciferase under the control of the p21 Waf1/Cip1 gene promoter. In conjunction with a noninvasive bioluminescent imaging technique, p21- p -luc mice enabled us to monitor the endogenous p21 Waf1/Cip1 gene expression in vivo . By monitoring and quantifying the p21 Waf1/Cip1 gene expression repeatedly in the same mouse throughout its entire lifespan, we were able to unveil the dynamics of p21 Waf1/Cip1 gene expression in the aging process. We also applied this system to chemically induced skin carcinogenesis and found that the levels of p21 Waf1/Cip1 gene expression rise dramatically in benign skin papillomas, suggesting that p21 Waf1/Cip1 plays a preventative role(s) in skin tumor formation. Surprisingly, moreover, we found that the level of p21 Waf1/Cip1 expression strikingly increased in the hair bulb and oscillated with a 3-week period correlating with hair follicle cycle progression. Notably, this was accompanied by the expression of p63 but not p53. This approach, together with the analysis of p21 Waf1/Cip1 knockout mice, has uncovered a novel role for the p21 Waf1/Cip1 gene in hair development. These data illustrate the unique utility of bioluminescence imaging in advancing our understanding of the timing and, hence, likely roles of specific gene expression in higher eukaryotes.

To investigate the potential functional cooperation between p27Kip1 and p130 in vivo, we generated mice deficient for both p27Kip1 and p130. In p27Kip1-/-; p130-/- mice, the cellularity of the spleens but not the thymi is significantly increased compared with that of their p27Kip1-/- counterparts, affecting the lymphoid, erythroid, and myeloid compartments. In vivo cell proliferation is significantly augmented in the B and T cells, monocytes, macrophages, and erythroid progenitors in the spleens of p27Kip1-/-; p130-/- animals. Immunoprecipitation and immunodepletion studies indicate that p130 can compensate for the absence of p27Kip1 in binding to and repressing CDK2 and is the predominant CDK-inhibitor associated with the inactive CDK2 in the p27Kip1-/- splenocytes. The finding that the p27Kip1-/-; p130-/- splenic B cells are hypersensitive to mitogenic stimulations in vitro lends support to the concept that the hyperproliferation of splenocytes is not a result of the influence of their microenvironment. In summary, our findings provide genetic and molecular evidence to show that p130 is a bona fide cyclin-dependent kinase inhibitor and cooperates with p27Kip1 to regulate hematopoietic cell proliferation in vivo.

We report the genome sequence of Theileria parva , an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum , and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated.

EtCRK2, a cyclin-dependent kinase from the coccidian parasite, Eimeria tenella is closely related to eukaryotic cyclin-dependent kinases that regulate progression of the cell cycle and to several cyclin-dependent kinases identified in the Apicomplexa. Northern blot analyses revealed that EtCRK2 is transcribed during both asexual (first-generation schizogony) and sexual (oocyst sporulation) replicative phases of the parasite life cycle. In addition, it appears to be transcriptionally regulated during meiosis. Recombinant EtCRK2 produced in Escherichia coli has kinase activity which is significantly stimulated by the addition of vertebrate cyclin A. This cyclin-dependent kinase may play a significant role in regulating critical cell cycle events during both asexual proliferation and sexual development of the parasite.

This paper presents a computational and theoretical investigation of the vacuum mechanosynthesis of di- amond on the clean C(110) surface from carbon dimer (C2) precursors positionally constrained throughout the reaction pathway by silicon- or germanium-doped triadamantane derivatives mounted on a scanning probe tip. Interactions between the dimer placement tools and the bare diamond C(110) surface are inves- tigated using Density Functional Theory (DFT) with generalized gradient approximation (GGA) by con- structing the reaction path potential energy profiles and analyzing ab initio molecular dynamics simulations. Similar methods are applied to study the energetics and kinetics of recharging the tool with acetylene. Molecular mechanics simulations on extended tool tips are carried out to elucidate the positional uncer- tainty of the carbon dimer due to thermal fluctuations, and the possibility of intermolecular dimerization and dehydrogenation of the dimer placement tools is explored.

The kinetics of elementary reactions involved in the chain chlorination of cyclopropane are examined using a combination of absolute and relative rate constant measurements and first principles ele...

Semiempirical direct dynamics simulations are used to study the potential role of CO in the gas-phase catalytic growth of carbon nanotubes. Calculations employing a fully self-consistent AM1 semiempirical electronic Hamiltonian predict that CO molecules can chemically adsorb to the open edge of partially grown zigzag and armchair nanotubes. The adsorbed CO molecules can form either pentagonal or hexagonal carbon rings by an electrocyclic reaction with neighboring adsorbed CO groups. Formation of hexagonal carbon rings in zigzag nanotubes is kinetically and thermodynamically favored by a CO insertion reaction with CO-saturated ends. These results provide some computational evidence that gas-phase CO can adsorb and contribute to the intermediate and latter stages of carbon nanotube growth. This study assumes that growth proceeds by the addition of carbon to the nanotube edge held open by metal catalyst particles, as opposed to a root growth or capped end growth mechanism.

The cyclin-dependent kinase (cdk) inhibitor p27(Kip1) is a central mediator in the imposition and maintenance of quiescence through the sequestration of G(1)-specific cyclin-cdk complexes. Previous studies have implicated the c-Jun co-activator protein Jab1 as a regulator of intracellular p27(Kip1) levels. Jab1 has been reported to interact with p27(Kip1) and cause its translocation to the cytoplasm as a prelude to the degradation of the cdk inhibitor. Here we describe experiments that showing phosphorylation of p27(Kip1) at serine 10 leads to the suppression of Jab1 levels with the concomitant inhibition of c-Jun-dependent transcription. This repression is minimized upon quiescence exit through the rapid and preferential loss of the serine 10-phosphorylated form of p27(Kip1) following serum stimulation. Our results, therefore, demonstrate an additional role for p27(Kip1) in the modulation of c-Jun-dependent transcription via Jab1.

Ab initio molecular dynamics simulations have been used to study the subpicosecond chemistry and dynamics of hyperthermal O(3P) collisions with single-walled carbon nanotubes, with a particular focus on insertion and substitutional doping. The barrier for inserting an O(3P) atom through the center of a hexagonal carbon ring was determined to be 13.7 eV, compared to an estimated dynamic effective barrier of 15.9 eV and a threshold energy on the order of 15–20 eV. Under similar conditions, collisions with a nanotube carbon atom are observed to generate oxygen substitutionally doped nanotubes and heptagonal carbon ring defects. At incident energies above the insertion threshold, an oxygen atom that passes through the center of a hexagonal carbon ring has the tendency to become accelerated and pass completely through the nanotube. Under thermal conditions the O(3P) atom binds to the nanotube without a barrier, leading to one of two products: an epoxide, and an adatom oxygenated nanotube. Tube curvature effects result in an increase of the epoxide binding energy with a decrease in tube diameter. However, no noticeable effects of tube diameter on insertion were established from the simulations.

The dynamics of friction and energy dissipation of a small nanoscale hydroxylated alumina surface sliding across a large identical surface were investigated by molecular dynamics (MD) simulations. The energy released into both the sliding and stationary surfaces and the energy transfer from the sliding interface to the bulk were investigated by monitoring the temperature of the surfaces and their sublayers. Steady state temperature gradients are found for the sublayers of each surface as a result of the balance between the heat released from the sliding friction and heat transfer to the bulk. The MD simulations show periodic friction energy release from the interface to the surfaces, giving rise to periodic changes in the temperature of the surface sublayers. This temperature depends on the sliding velocity. The periodicity in the friction energy release arises from the periodic unit cell structures of the surfaces. Atomic-level vibrational motions and interdigitation of the surface atoms give rise to the frictional energy of the sliding surfaces. Velocity distributions are determined for atoms within different surface layers and they become more Boltzmann-like the further the layers are from the interface and if the sliding is fast and not in the stick–slip regime. Tribological properties for continuous sliding across the same regime of the bottom surface, by using periodic boundary conditions, differ from those for sliding across a large bottom surface.

Clickable co-substrate: A tri-functional 5'-γ-ferrocenyl adenosine triphosphate (Fc-ATP) derivative containing a clickable site was synthesized. This compound is an effective co-substrate in kinase-catalyzed phosphorylation reactions, which can be detected by both electrochemical and immunoassay detection methods. The clickable reaction site makes direct modification possible, which greatly expands its application.