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C M Chiang

Publications and source records attributed to C M Chiang.

At least 19 recordsLinked to original sources

Properties of PC4 and an RNA polymerase II complex in directing activated and basal transcription in vitro.

A human RNA polymerase II (pol II) complex was isolated from a HeLa-derived cell line that conditionally expresses an epitope-tagged RPB9 subunit of human pol II. The isolated FLAG-tagged pol II complex (f:pol II) contains a subset of general transcription factors but is devoid of TFIID and TFIIA. In conjunction with TATA-binding protein (TBP) or TFIID, f:pol II is able to mediate both basal and activated transcription by Gal4-VP16 when a transcriptional coactivator PC4 is also provided. Interestingly, PC4, in the absence of a transcriptional activator, actually functions as a repressor to inhibit basal transcription. Remarkably, TBP is able to mediate activator function in this transcription system. The presence of TBP-associated factors, however, helps overcome PC4 repression and further enhance the level of activation mediated by TBP. Alleviation of PC4 repression can also be achieved by preincubation of the transcriptional components with the DNA template. Sarkosyl disruption of preinitiation complex formation further illustrates that PC4 can only inhibit transcription prior to the assembly of a functional preinitiation complex. These results suggest that PC4 represses basal transcription by preventing the assembly of a functional preinitiation complex, but it has no effect on the later steps of the transcriptional process.

HeLa Cells

Analysis of binding of cobra cardiotoxins to heparin reveals a new beta-sheet heparin-binding structural motif.

Heparin and heparan sulfate have recently been shown to bind to snake cardiotoxin (CTX) and to potentiate its penetration into phospholipid monolayer under physiological ionic conditions. Herein we analyze the heparin-binding domain of CTX using 10 CTXs from Taiwan and African cobra venom. We also performed computer modeling to obtain more information of the binding at molecular level. The results provide a molecular model for interaction of CTX-heparin complex where the cationic belt of the conserved residues on the concave surface of three finger beta-sheet polypeptides initiates ionic interaction with heparin-like molecules followed by specific binding of Lys residues near the tip of loop 2 of CTX. The dissociation constants of CTXs differ by as much as 4 orders of magnitude, ranging from approximately 140 microM for toxin gamma to approximately 20 nM for CTX M3, depending on the presence of Lys residues near the tip of loop 2. High affinity heparin binding becomes possible due to the presence of Arg-28, Lys-33, or the so-called consensus heparin binding sequence of XKKXXXKRX near the tip of the loop. The well defined three-finger loop structure of CTX provides an interesting template for the design of high affinity heparin-binding polypeptides with beta-sheet structure. The finding that several cobra CTXs and phospholipase A2 bind to heparin with different affinity may provide information on the synergistic action of the two venom proteins.

Amino Acid Sequence

Crystal structure of cardiotoxin V from Taiwan cobra venom: pH-dependent conformational change and a novel membrane-binding motif identified in the three-finger loops of P-type cardiotoxin.

The crystal structure of cardiotoxin V from Taiwan cobra venom (CTX A5) has been solved at pH 8.5 and refined to an R-factor of 20.7% for 7013 reflections [>2sigma(F)] between 8- and 2.19-A resolution. The refined model shows that CTX A5 exists as a dimer. The assembly consists of 974 non-hydrogen atoms from 124 residues and 73 water molecules. The global monomeric structure is similar to that determined by NMR at pH 3.7, characterized by a core formed by two beta-sheets connected with three-finger loops. However, local conformational differences are detected in two functionally important regions, loops I and II. A disparity between the NMR and X-ray structure of CTX A5 is detected near the tip of loop I and can be attributed to the difference in the protonation state of His4 at different pH, resulting in a reorientation of the His4 imidazole ring. A concerted motion of amino acid side chains located near His4 is detected and possibly contributes to the pH-dependent binding ability of CTX A5 to phospholipid model membranes. The second difference, detected at the tip of loop II, is due to the hydrophobic contact between CTX dimers in the crystal packing and the interaction of water molecules with amino acid residues in the loop II region of the CTX containing Pro31 (P-type CTX). This interaction forces loop II into a more rigid omega shape bridging the main chain at positions 27 and 34, contradictory to the flexible, tapering shape detected by NMR. Thus, a novel continuous hydrophobic column capable of binding to and possibly penetrating the membrane lipid bilayer is formed by the tips of the three-finger loops. In this respect, the X-ray crystal structure of CTX A5 may represent the CTX structure in the membrane-binding mode.

Amino Acid Sequence

Heparin and heparan sulfate bind to snake cardiotoxin. Sulfated oligosaccharides as a potential target for cardiotoxin action.

Cardiotoxins (CTXs) from cobra venom show cytotoxicity toward several cell types. They cause systolic heart arrest and severe tissue necrosis. Their interaction with phospholipids is established but by itself fails to explain the specificity of these toxins; other component(s) of membrane must, therefore, intervene to direct them toward their target. We herein show, for the first time, that sulfated glycosaminoglycans, heparin, heparan sulfate (HS), chondroitin sulfate (CS), and dermatan sulfate (DS), interact with CTX A3, a major component of Taiwan cobra venom, by use of affinity chromatography, circular dichroism, absorbance, and fluorescence intensity and anisotropy measurements. The relative strength of binding, determined by the NaCl concentration required to dissociate the CTX-glycosaminoglycan complex, varied as follows: heparin > DS > CS > HS. In physiological buffer (8 mM Na2HPO4, 2.7 mM KCl, 1.8 mM KH2PO4, 138 mM NaCl, pH 7.4), however, only heparin and HS bound to CTX, with respective dissociation constants of 1.4 and 16 microM, while CS and DS failed to exhibit well defined binding behavior, as indicated by fluorescence measurements. We estimate that CTX makes 3-4 ionic contacts with heparin based on a salt-dependent binding study and that approximately 40% of binding free energy is derived from purely electrostatic interactions under physiological conditions. Sulfated pentasaccharide may be sufficient to bind to CTX. We also found that heparin accentuates the penetration of CTX into phospholipid membranes as analyzed by Langmuir monolayer measurement. In view of these results we propose that heparin-like moieties of the cell surface may modulate the action of CTX.

Binding Sites

Localization of T cells, interferon-gamma and HLA-DR in eutopic and ectopic human endometrium.

OBJECTIVES: Immunologic mechanisms are implicated in the pathogenesis of endometriosis and endometriosis-associated reproductive failure. The purpose of this study was to describe key immune response elements in eutopic and ectopic endometrium and to test the hypothesis that expression of CD3-positive T cells, the T-helper 1-type cytokine, IFN-gamma, and the antigen presentation marker, HLA-DR, vary throughout the menstrual cycle in eutopic endometrium and are more abundantly expressed in ectopic than in eutopic endometrium. METHODS: Eutopic and ectopic endometrium obtained at hysterectomy from 7 women with endometriosis were compared with hysterectomy specimens from 7 women with adenomyosis and 10 women without endometriosis or endometrial pathology. Tissues were formalin-fixed, paraffin-embedded, sectioned and stained using the biotin-streptavidin-alkaline phosphatase technique and antibodies to human CD3, IFN-gamma, and HLA-DR. Eutopic endometrial samples were histologically divided into menses (n = 5), proliferative (n = 9), and secretory (n = 10) phases. Positive control tissues (spleen) and negative controls (no primary antibody) were used in each experiment. RESULTS: T cells, IFN-gamma and HLA-DR-positive cells were observed in eutopic endometrial samples throughout the menstrual cycle. Glandular epithelium was CD3-negative except for CD3-positive cells surrounding and occasionally interdigitating between glandular epithelium. Glandular epithelium was IFN-gamma-positive and HLA-DR-positive in all phases except the proliferative phase. Staining was more often observed in the basalis than in the functionalis layer, ranging from patchy staining to the entire gland. T cells, IFN-gamma, and HLA-DR-positive stromal cells were more abundant in secretory endometrium than in proliferative samples. CD3, IFN-gamma, and HLA-DR-positive cells were scattered throughout the myometrium and concentrated in vessels. Higher intensity staining was observed in ectopic than in eutopic endometrium, with CD3 and HLA-DR-positive cells forming aggregates around IFN-gamma and HLA-DR-positive glands. The intensity of IFN-gamma staining in ectopic endometrium was similar to the intensity of staining observed in menstrual and late secretory basalis samples from eutopic endometrium. CONCLUSIONS: The results of this observational study suggest that activated T cells, IFN-gamma and upregulation of antigen presentation may play a role in normal endometrial physiology. The increased number of T cells, expression of IFN-gamma, and enhanced antigen presentation in ectopic compared to eutopic endometrium support the concept that cellular immune activation is involved in endometriosis and its sequelae.

Adult

Topology and reorganization of a human TFIID-promoter complex.

Transcription factor TFIID is a multiprotein complex composed of a TATA-box-binding subunit, TBP, and several tightly associated factors (TAFs). Human TFIID-promoter interactions are restricted to the TATA-box region on most core promoters but extend over a large promoter region downstream of the TATA box and the transcription start site on the Ad2ML promoter. TFIID downstream interactions are thought to be functionally relevant because they can be induced by transcriptional activators, which in some cases requires TFIIA, result in stabilization of the TFIID-promoter complex, and correlate with increased recruitment of the remaining general transcription factors. Here we examine the topological organization of human TFIID complexes bound to the Ad2ML promoter. Our data provide insight into the relative disposition of DNA and several TFIID subunits, as well as evidence for DNA wrapping by TFIID, and suggest a direct role of TFIIA in the stable positioning of promoter DNA relative to TAFs.

Crystallography, X-Ray

Conformational change and inactivation of membrane phospholipid-related activity of cardiotoxin V from Taiwan cobra venom at acidic pH.

The phospholipid binding activity of cardiotoxin V from Naja naja atra (CTX A5) was studied by use of Langmuir monolayers and found to exhibit pH-dependence in binding to phosphatidylcholine membrane with an apparent pKa around 6.0. Proton NMR investigation of the CTX A5 molecule in the presence of phosphatidylcholine micelles reveals a decrease in association of CTX A5 with membranes at low pH as a result of the protonation of His-4 near the membrane binding site of loop I region of CTX. The pH-dependent binding can be attributed mainly, but not solely, to the change in charge content of the CTX molecule upon His-4 protonation at the membrane/water interface. This is shown by analyzing the pH- and ionic strength dependence of binding of CTXs to phospholipid monolayers according to Gouy-Chapman theory. The protonation of the His-4 residue also results in a local conformational change in the loop I region since the chemical shifts of amide protons for the amino acid residues from Cys-3 to Thr-14 are all found to vary as a function of pH with an apparent pKa similar to that of His-4. Interestingly, the effect is relayed to other amino acid residues in the structural core of the protein such as those in C-terminal (Lys-60, Cys-61, and Asn-62) and triple-stranded antiparallel beta-sheet (Cys-22, Lys-24, Ala-25, Arg-38, and Ala-41) regions. An additional local conformational change in the molecule results around pH 5 as evidenced by circular dichroism spectroscopic studies, although this change does not affect the characteristic beta-sheet and three-finger loop structure of CTX molecule as revealed by two-dimensional NOESY 1H NMR study. The latter conformational change at acidic pH, however, completely inactivates CTX-induced aggregation/fusion activity of sphingomyelin vesicles. The results suggest that deciphering the functional sites of CTXs on the basis of structure and dynamics determined at low pH should be done with caution. Since 19 out of 44 CTX homologues with known amino acid sequence contain His-4, the effect of His-4 on the structure and function of CTX molecules is important and is discussed in terms of the diverse membrane targets of CTX subtypes. Also discussed is the pH-induced activation of snake venom proteins in the victim.

Animals

The role of acidic amino acid residues in the structural stability of snake cardiotoxins.

We have recently shown that membrane-related activities of cardiotoxin V from Naja naja atra (CTX A5) are diminished at acidic pH although the overall beta-sheet structure of the molecule is maintained. In order to understand more about the mechanism of inactivation of CTX at acidic pH, we studied the effect of pH and denaturing reagents on the structural stability of CTX. We found, first, pH-induced structural transitions occurred in CTX A5 at two pH values as judged by the CD ellipticity around 195 nm: an increase in the beta-sheet content occurred around pH 4 and followed by a decrease, therein, around pH 2. The pKa of three acidic amino acid residues in CTX A5, i.e., Glu-17, Asp-42, and Asp-59, were determined to be 4.0, 3.2, and below 2.3, respectively, by NMR spectroscopy. The low pKa value of Asp-59 implies salt bridge formation between Lys-2 and Asp-59. Thus, electrostatic interaction may stabilize the three loop structure in addition to the hydrogen bonds between N- and C-termini of CTX molecule. Second, 2,2,2-trifluoroethanol (TFE) and guanidinium chloride (GdmHCI) were found to induce alpha-helical and random coil formation, respectively, in CTX A5 and eight other beta-sheet CTXs. Comparison of the relative potencies of TFE and GdmHCI to induce structural changes suggests that the amino acid residue located at position 17 plays a role in the structural stability. Specifically, CTXs containing negatively charged Glu-17 are least stable. It is suggested that Glu-17 may perturb the interaction between Lys-2 and Asp-59, and thus the overall stability of beta-sheet, in the presence of denaturing reagent. In conclusion, the perturbed structural stability of CTXs may partially explain the lower activity CTX exhibits at acidic pH. A structural model to account for the unfolding and refolding of CTX molecules without the breaking of disulfide bonds is also proposed.

Amino Acid Sequence

A histone octamer-like structure within TFIID.

The general transcription factor TFIID nucleates initiation complex formation through direct core promoter binding, commits promoters within chromatin to transcription, and mediates the action of transcriptional activators, a phenomenon that may correlate with enhanced TFIID recruitment or conformational changes in TFIID-promoter complexes. Molecular studies of the multiprotein TFIID complex have identified a primary TATA binding subunit (TBP), TBP-associated factors (TAFs) that interact with and mediate the function of activators and intersubunit interactions but have yielded relatively little insight into the structural organization of the complex or the actual mechanism of transcriptional activation. Here we present biochemical evidence for the structural relevance of histone homologies in the human TFIID subunits hTAF80, hTAF31 and hTAF20/15. Together with analyses of native TFIID complexes and accompanying crystallographic studies, the results suggest that there is a histone octamer-like TAF complex within TFIID.

Amino Acid Sequence

Augmented two-channel arrhythmia detection: an efficient diagnostic method for implantable devices.

ICDs are highly effective in preventing sudden cardiac death. However, inappropriate device shocks caused by false-positive diagnoses are estimated to happen in 20% of all patients. The need for implantable electrical devices to detect with precision arrhythmias requiring therapy has spawned a variety of proposals for better means of tachycardia identification. To address this problem, the augmented two-channel arrhythmia detection (A2CAD) algorithm, a real-time scheme utilizing timing and morphology from both the atrial and ventricular channels, is introduced. The algorithm uses rate detection as a first stage and augments this with morphological signal analysis in rhythms that confound the rate only diagnoses. The software executes in real-time (online), and has been tested on 60 passages of two-channel intracardiac signals. The following arrhythmias constituted the test set: 10 AF and/or atrial flutter; 15 SVT; 16 VT; 10 ventricular flutter or VF; 5 sinus tachycardia; and 4 cases of AF concurrent with VF. Results from 60 patient cases indicate 57 (95%) of 60 success rate for A2CAD, validating its potential for implementation in future implantable devices.

Algorithms

Establishment of stable cell lines expressing potentially toxic proteins by tetracycline-regulated and epitope-tagging methods.

A tetracycline-regulated expression system is combined with the FLAG-epitope tagging method for conditional expression of potentially toxic proteins in mammalian cells. This strategy allows a controlled expression of exogenous gene products and also provides a unique way of protein purification. Two mammalian expression plasmids containing the FLAG sequence and flanking multiple cloning sites were created for conditional protein expression. The cDNAs encoding human basal transcription factors TBP, TAFII55 and the p62 subunit of TFIIH were individually cloned into these vectors and introduced into a HeLa-derived cell line that constitutively expresses a tetracycline-regulated transactivator (tTA). The established clonal human cell lines express FLAG-tagged basal transcription factors in a manner modulated by the amount of tetracycline in the growth medium. In the absence of tetracycline, tTA binds to the DNA recognition sites of the expression plasmid and induces the expression of tagged proteins. When tetracycline is added back to the growth medium, the induced protein starts to decay. This provides us with an estimation of the in vivo half-lives of TBP and TAFII55, which were assessed to be less than 20 and 6 hours, respectively, in HeLa cells. The level of induced proteins in the absence of tetracycline could be further enhanced by including the antibiotic G418 to presumably boost the production of tTA which in turn activates the expression of tagged proteins.

Base Sequence

Cloning of an intrinsic human TFIID subunit that interacts with multiple transcriptional activators.

TFIID is a multisubunit protein complex comprised of the TATA-binding protein (TBP) and multiple TBP-associated factors (TAFs). The TAFs in TFIID are essential for activator-dependent transcription. The cloning of a complementary DNA encoding a human TFIID TAF, TAFII55, that has no known homolog in Drosophila TFIID is now described. TAFII55 is shown to interact with the largest subunit (TAFII230) of human TFIID through its central region and with multiple activators--including Sp1, YY1, USF, CTF, adenoviral E1A, and human immunodeficiency virus-type 1 Tat proteins--through a distinct amino-terminal domain. The TAFII55-interacting region of Sp1 was localized to its DNA-binding domain, which is distinct from the glutamine-rich activation domains previously shown to interact with Drosophila TAFII110. Thus, this human TFIID TAF may be a co-activator that mediates a response to multiple activators through a distinct mechanism.

Adenovirus E1A Proteins

TATA-binding protein-associated factor(s) in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter.

The RNA polymerase II (Pol II) basal transcription factor TFIID is composed of the TATA box-binding protein (TBP) and several TBP-associated factors (TAFs). TBP is required for Pol II transcription from TATA-containing and TATA-less promoters. TATA-less promoters of mRNA-encoding genes often contain an initiator element at the transcription start site that is sufficient to direct accurate Pol II transcription. Here we address the mechanisms of functional TBP recruitment to the TATA-less initiator-dependent promoter of the mouse terminal deoxynucleotidyl transferase (TdT) gene. We show that the natural TATA-less TdT initiator region is sufficient to promote low levels of specific transcription in vitro and to direct the assembly of a stable preinitiation complex. In contrast to what is observed for several other promoters lacking a consensus TATA element, the TATA-binding activity of TBP is not required for the functional recruitment of TFIID to the natural TATA-less TdT and beta-polymerase promoters. Moreover, a comparison of TBP and highly purified epitope-tagged TFIID reveals that one or several TAFs function independently of distal regulatory elements to mediate initiator-directed (basal) transcription from the natural TATA-less TdT core promoter in crude nuclear extracts. Furthermore, by using a transcription system reconstituted with purified components, we present the first evidence for a basal transcription function of TAFs through the TdT initiator element. Altogether, our results suggest an alternative pathway for TFIID recruitment to initiator-dependent TATA-less class II promoters in which TAF(s) recruit TBP by interacting either directly or indirectly with the initiator region.

Base Sequence

Two distinct types of cardiotoxin as revealed by the structure and activity relationship of their interaction with zwitterionic phospholipid dispersions.

Cardiotoxins (CTXs) are a group of homologous proteins found in cobra snake venom and consist of 60-62 amino acid residues. Although CTXs are known to consist of three extended beta-sheet loops similar to neurotoxins, the target and interaction of CTXs with membranes unlike those of neurotoxins are not well understood. Herein, we report comparative studies of 10 CTXs purified from Taiwan cobra (Naja naja atra) and Mozambique spitting cobra (Naja mossambica mossambica) snake venoms with respect to their interactions with zwitterionic phospholipids. Based on the CTX-induced mixing of sphingomyelin vesicles and the binding of CTX to lysophosphatidylcholine micelles, two distinct types of CTX, i.e. P- and S-type CTX, are identified. P-type CTXs are characterized by the presence of Pro-31 within a putative phospholipid binding site near the tip of loop 2; whereas S-type CTXs are characterized by the presence of Ser-29 within the same but more hydrophilic region. Although binding of all CTXs to phospholipid membranes involves a phospholipid binding site at loop 1, P-type CTXs exhibit higher fusion and binding activity than S-type CTXs, presumably due to the additional phospholipid binding site at loop 2. The binding modes of P- and S-type CTX are thus different. Analysis of the primary structures of 46 CTXs from the genus Naja indicates that these two types of CTXs exist in all species examined. Reasonable structure/activity correlation can be detected for the effects of CTXs on muscle and red blood cells, although notable exceptions are also found. S-type CTXs are generally found to exhibit higher muscle cell depolarization activity, whereas P-type CTXs are found to possess a higher hemolytic activity. Thus the mechanism of action of CTXs seems to involve CTX-membrane interactions and depends on the type of the cell membrane and CTX molecules under study. The two lipid binding sites in P-type CTXs and one lipid binding site in S-type CTXs show large variation in their amino acid residues, but they do display some common distribution of residue type. Analogous to the signal sequences for protein import, these regions are characterized by the coexistence of an exposed hydrophobic surface flanked on either side by a cationic residue. A hypothesis is proposed to explain the general cytotoxic and specific cardiotoxic effect of CTXs based on the two CTX subtypes in snake venom.

Amino Acid Sequence

Direct interaction of human TFIID with the HIV-1 transactivator tat.

The tat gene of the human immunodeficiency virus (HIV) plays a central role in the activation and life cycle of HIV. The tat protein (Tat) specifically transactivates HIV transcription in vivo and in vitro, exerting its effects at the level of transcriptional initiation and elongation. Here we report that Tat binds directly to the basal transcription factor TFIID. The transcriptional activity of HeLa extracts was depleted after chromatography on a Tat affinity column, which specifically retained the polymerase II-specific factor TFIID. Direct interaction of Tat with holo-TFIID, composed of TATA-binding protein (TBP) and associated factors (TAFs), was observed. Tat binds, through amino acids 36-50, directly to the TBP subunit of TFIID. Our results suggest that Tat may transduce upstream or downstream regulatory signals by direct interaction with the basal transcription factor TFIID.

Base Sequence

Discrimination of ventricular tachycardia from sinus tachycardia by antitachycardia devices: value of median filtering.

Rate and rate variation algorithms used by implantable devices designed for management of life-threatening arrhythmias have major limitations in separating physiologic sinus tachycardia (ST) from pathologic ventricular tachycardia (VT) requiring therapy. These algorithms presently utilize criteria such as simple heart rate, stability of rate, or derivative of rate (sudden onset) which assumes a gradual onset for ST and an abrupt onset for VT. An alternative method employing median filtering was designed, tested, and compared to a previously published sudden onset rate algorithm using the same data set for analysis of performance. In 50 patients, the onset of ST during exercise and onset of VT were analysed. To accommodate occasional outlying intervals which might affect rate derived by averaging, a five-cycle median filter was used to smooth heart rate. Results from using a 'fixed-interval' or a 'percent' change in the median gave better discrimination of ST and VT than previously published 'fixed-interval' or 'percent' change algorithms. The superiority of median filtering performance was validated by statistical measures.

Algorithms

Automated analysis of spontaneously occurring arrhythmias by implantable devices. Limitations of using rate and timing features alone.

Real-time automated systems for arrhythmia analysis by implantable antitachycardia devices have been designed to incorporate two-channel rate criteria with intracavitary atrial and ventricular electrogram morphology. Because the power requirements for morphologic analysis substantially limit antitachycardia device longevity, the authors sought to develop an alternative algorithm that relies solely on rate and three newly developed timing features: onset (median ventricular rate filtering to detect abrupt onset), loss of atrioventricular (AV) sequency (premature ventricular depolarizations), and regularity-multiplicity (minimal median cycle length variation concurrent with integral [n:1] AV periodicity). This system was assessed using spontaneously occurring arrhythmias in patients undergoing electrophysiology studies. Electrograms were captured on FM tape (1-500 Hz) using biopolar catheters in the high right atrium and the left ventricular apex. In 11 patients, 25 distinct arrhythmias were analyzed, which included sinus tachycardia (ST) (1 passage), supraventricular tachycardia (SVT) (6 passages), ventricular tachycardia (VT) with concurrent sinus rhythm (16 passages), VT with concurrent atrial flutter (VT/AFl) (2 passages), and ventricular fibrillation (VF) (1 passage). The algorithm correctly diagnosed 1 of 1 episode of ST, 4 of 6 episodes of SVT, 15 of 16 episodes of VT with concurrent sinus rhythm, 0 of 2 episodes of VT/AFl, and 1 of 1 episode of VF. Ventricular tachycardia episodes were misdiagnosed as SVT because of absence of loss of AV sequency in VT onset (1 episode), presence of multiplicity between VT and AFl (1 episode), and absence of VT regularity during AFl (1 episode).(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms