bluuebunny/crossref_metadata_2025 huggingface dataset:
The Funeral Speech, A Study of Values
Authors: Walcot P.
Published: July 2013

Since no one doubts the pre-eminence of Socrates as a teacher, there is much, presumably, to be said in favour of his method of instruction. The picture of Socrates to be gained from the earlier dialogues of Plato is one of a man who consistently challenged orthodox opinions. In the same way, but, of course, with nothing like the Athenian's skill, I propose in what follows to react against a commonly accepted view; to be precise, I wish to scrutinize the opinion that the Funeral Speech, delivered by Pericles at the end of the first year of the Peloponnesian War and known to us from Thucydides, presents the reader with a splendid portrait of fifth-century Athens, and that, in stressing the spirit rather than the forms of Athenian democracy, it qualifies as the ancient equivalent of Lincoln's Gettysburg Address. We all idealize the ancient Greeks; we ignore the harsh realities and prefer to concentrate our attention on what we see as the grandeur of Aeschylus, the splendour of the Parthenon, and the vision of Pericles; and it is the Funeral Speech, beyond everything else in Greek literature, which allows us to indulge in this type of escapism. That the Funeral Speech does have a ‘glorious’ reputation is a fact. Does it deserve so uncritical a fame ? If this question is posed, I ask it not from any perverted desire to debunk its reputation, but simply in order to gain a deeper understanding not only of the speech but also of the Greeks to whom it was addressed and of the particular statesman who delivered it.
Hybris and Dishonour: I
Authors: Fisher N. R. E.
Published: July 2013

Professor D. M. MacDowell's article continues a recent and welcome tendency to question the common interpretation of hybris by study of the actual instances of the concept throughout Greek literature. MacDowell's definition ‘having energy or power and misusing it self-indulgently’ is fairly broad, and he supports it by five further points:

i) that hybris is always bad,

ii) that it is always voluntary,

iii) that it is frequently, but not always, produced by such things as youth, wealth, and excess of food and drink,

iv) that it is not usually religious, and

v) that it often involves a victim, and is more serious when it does.
The Followers of Peisistratus
Authors: Holladay James
Published: July 2013

The names and natures of the three parties which struggled for power in early-sixth-century Athens have puzzled scholars both ancient and modern. The paucity and murkiness of the evidence have made progress difficult and the decisive contribution to the solution of the problem most probably lies in the hands of the archaeologists and the epigraphists. In the meantime some scholars have retreated into agnosticism. ‘The reasons for Athens' rejection of the Solonian solution are, except in broadest outline, lost.’ Scepticism is clearly an important tool in the handling of inadequate evidence, but the present article is written in the belief that some clarification of the problem is still possible with the existing evidence.
Aristocracy and its Advocates in Archaic Greece
Authors: Greenhalgh P. A. L.
Published: July 2013

The subject of this article is the appearance in archaic Greek literature of the two basic principles of aristocracy as a form of government—republicanism and noble rule—and how they were upheld, augmented, qualified, idealized, and justified against the alternatives of monarchy and the aspirations of non-nobles either to join or disestablish the nobility as the ruling class. When Greek states emerged from the Dark Ages into the clearer light of history in the eighth and seventh centuries b.c., monarchy had almost everywhere given way to aristocracy. More or less exclusive groups of noble families had learnt, in Aristotle's phrase, ‘to take turns in ruling and being ruled’. The formation of the first republics required no change in the ideological climate of the unquestioning acceptance of the noble monopoly of wealth and privilege which we find in Homer and Hesiod, and similarly no change in this climate was required before republican governments were likely to be challenged. The Homeric nobleman's primary obligation, simply expressed in Hippolochus' parting injunction to his son ‘always to be best’, runs contrary to the principle of equals taking turns in ruling and being ruled, and it would not be surprising if many a Greek aristocrat acquiesced in being equal best only because he lacked the opportunity to make himself single best. And where there were narrow aristocracies which by their exclusiveness made permanent political inferiors of noble families which were the socio-economic peers of the politically privileged, as in Corinth under the Bacchiads or Mytilene under the Penthilids, there was likely to be a greater incentive for an ambitious nobleman to usurp for his own family the corporate constitutional superiority of his privileged rivals; and there might be correspondingly less ideological opposition from noble republicans so far as other politically unprivileged nobles would be constitutionally no less deprived under a tyrant, and might have much to gain in power and wealth from supporting the overthrower of the exclusive regime. The disappearance of Dark Age kingship of the Homeric primus inter pares type is nowhere likely to have generated all at once an ideology which made monarchy an anathema. The Homeric king is not even distinguished from the other nobles by a title which is not also enjoyed by the heads of other great houses, and the lack of traditions about the disappearance of kingship suggests that it was undramatic. On the other hand, because tyranny (in the basic sense of an autocracy established in a state which had been a republic) necessarily meant permanent constitutional inferiority for social equals, acquiescence in even a benign and initially popular autocracy was likely to wane once the possibility of constitutional equality had been discovered (however narrow the ruling circle of equals had been).
Socrates and Authority
Authors: Mulgan R. G.
Published: July 2013

In a well-known passage in the Apology, Socrates says that if the court release him on condition that he give up questioning the views of his fellow citizens, he will refuse to obey:

… If you say to me, ‘Socrates, this time we will not follow Anytus but will let you go on condition that you no longer spend your time on this inquiry and stop philosophizing; if you are caught doing this again, you shall die’—if you were to acquit me on this condition, I would reply: ‘Men of Athens, I honour and love you, but I shall obey the god rather than you and as long as I breathe and have the capacity I shall never cease philosophizing …’ (29 c 6–d 5.)
Dramatic Speech in the Roman Historians
Authors: Miller N. P.
Published: July 2013

Inspite of much sensible writing, by many scholars, on the real importance and significance of the literary convention, there remains among some students of the Classics a persistent folk-memory which asserts that speeches in the ancient historians are rhetorically decorative, deliberately deceptive, and historically inessential. That a speech can be one (or all) of these things is inarguable: but to assume that all speech in historical writing can be so dismissed is dangerous, because such assumption inhibits a full understanding of what a serious ancient historian may be trying to do with it. I should therefore like to look again at the convention, and at some of the ways in which it is used by the major Roman historians.
Roman Historians and the Roman Coinage
Authors: Shotter David
Published: July 2013

There is no novelty in suggesting the importance of Roman coins as a source for the study of Roman history; a considerable number of works have explored the possibilities of the subject. The chief problem, however, has always lain in appreciatinghow farthey can take us in an understanding of events: the coins are after all often as tendentious as the literary sources are sometimes alleged to be–or even more so. Further, when the historian moves from attempting to explain the legends to such matters as interpreting features of the portraiture, he is moving on to very subjective ground: for example, what may be the significance of the fact that on Nerva's Divvs Avgvstvs coins, the portrait of Augustus begins to look uncannily like that of Nerva himself? Or again, what are we to make of the fact that the obverse portrait on early coins of Trajan bears a resemblance to that of Nerva?
Modern Idiom in an Ancient Context
Authors: Donaldson G. H.
Published: July 2013

Since the Second World War we have been subjected to a flood of memoirs and counter-memoirs by generals, admirals, air marshals, and politicians. One of the direct results of this is that our vocabulary has been increased—if not enriched—by a military jargon. Most of the latter's terms have in fact very specialized meanings, and if they are used out of their proper context they can present a highly coloured view of a rather simple situation. Can these terms be applied with validity to historical situations of antiquity ? At first sight there is an attraction in theirvery modernity, for they seem to give a freshness of approach; but Professor Salmon's use of them in his recent article, ‘The Strategy of the Second Punic War’, has made the dangers of their use manifestly clear. By his use of these anachronisms—for that is surely what they are—Professor Salmon has given nothing new in the way of interpretation, but merely provided confirmation of Oman's dictum ‘Historians may have the most divergent views according to their predispositions’, and has exaggerated the capabilities of both sides beyond belief.
Two Implications of the Trojan Legend
Authors: Gossage A. J.
Published: July 2013

It is a well-known fact that the Trojan legend provided Augustus, as it had provided Julius Caesar before him, with a means of claiming divine ancestry. Likewise the Roman people were made the descendants of a nation renowned for its former greatness and celebrated by Homer. While much attention is paid to these facts, certain implications of the legend, for which apologies were sometimes felt (especially by Virgil) to be necessary, tend to pass unnoticed. One of these is that if the gens Iulia was descended from Aeneas, it possessed in him an ancestor whose birth was admittedly divine, but whose feats of valour were decidedly overshadowed in the Iliad by those of Hector. The other implication which I wish to discuss here is that if the Romans were descendants of the Trojans, it was from a defeated nation that the conquerors of the Mediterranean world had arisen. Was the Trojan heritage, in fact, despite its obvious value as propaganda, something of which the Romans and the emperor himself could justifiably be proud?
Plato for the Uninitiated
Authors: Carroll K. M.
Published: July 2013

Plato is the world's greatest philosopher, far transcending those who went before and a pattern to those who have come after. No other philosophical writer has had such enduring value and interest. He has been, down the ages, the companion and friend of the world's great thinkers and poets; for, though he lived in a world that, compared with our own with its vast resources of travel and knowledge, seems small and primitive, he is unique among men who have endeavoured to teach the things that matter, that are permanent. He ventured into realms of thought never before approached and had to find Greek words to match his thought while as yet the language had no technical phraseology. This tends to make some of the important theories he expounds difficult to grasp. But the dialogue form in which he wrote, the characterization of which he was master, and the vivid illustrations that light up his teaching awaken in the reader intense interest and help to make easier the task of following Plato in his ‘speculation upon all time and all place’, which he tells us is Philosophy.
Unknown Latin Literature
Authors: Dudley D. R.
Published: July 2013

One of the features of classical scholarship during the last ten years has been a renewal of interest in Latin literature. In England, at least, this was at a low ebb between the two great wars. The literature of Rome was regarded as derivative and second-rate. Virgil was the unwilling prisoner of the Augustan propaganda machine, Horace the favourite poet of those with no feeling for poetry, Ovid (apart from the Ars Amatoria) no more than a verse-writer of fatal facility, Plautus a knock-about comedian, and Terence a bore. Apart from Catullus, Lucretius, Petronius, and Tacitus, Latin could play no cards that Greek could not instantly trump. I do not think this an unfair picture of the impression of Latin literature I was given as an undergraduate. Why this was so is less easy to say. Partly, perhaps, because Oxford and Cambridge produced a succession of great expositors of Greek literature at a time when many of their Latin colleagues seemed immersed in the more arid forms of textual scholarship. Partly, again, because the iconoclasm of the age found in Latin a profitable and easy target.
The Deaths of Hector and Turnus
Authors: West David
Published: July 2013

This article is an attempt to throw light on Virgil's narrative of the death of Turnus by comparing it to Homer's narrative of the death of Hector. It will begin with a summary of these two episodes.
Plots and Politics in Aeschylus
Authors: Costa C. D. N.
Published: July 2013

The purpose of this article is to examine the extent to which Aeschylus may have altered the forms or emphases of the traditional plots which he used in the Oresteia and the Supplices and to decide whether we are justified in interpreting any such adjustments as a commentary on recent or contemporary politics. Much of what follows is not, of course, new; but a fresh analysis of the old evidence will, I hope, show that rather than take sides strongly in political disputes, Aeschylus chose to suggest how men ought to approach problems of public life and solve them in the best interests of all.
Some Thoughts on Translation
Authors: Rees B. R.
Published: July 2013

The history of classical scholarship bears the traces of many a violent battle over the theory and practice of translation. It is not surprising therefore that today, when translations are in more common use than ever before, not only as aids to reading the original but even as sole texts for pupils in schools and universities lacking the classical languages, their function and quality should be subjects of considerable discussion and disagreement. The demand is greater than ever, and a Penguin version of Homer can become a best-seller; but it is also harder than ever to satisfy oneself that the translation one has recommended is not misleading students nurtured in a culture and attuned to an idiom so different from those of the Graeco-Roman world. In the last quarter of the twentieth century the provision of good translations is a matter no longer of theoretical discussion but of immediate practical importance, if our students are to have the remotest possibility of reaching understanding of what classical writers were trying to say.
Experimental indications for Markov properties of small-scale turbulence
Authors: RENNER CHRISTOPH , PEINKE J. , FRIEDRICH R.
Published: July 2013

We present a stochastic analysis of a data set consisting of 1.25 × 107 samples
of the local velocity measured in the turbulent region of a round free jet. We find
evidence that the statistics of the longitudinal velocity increment v(r) can be described
as a Markov process. This new approach to characterize small-scale turbulence
leads to a Fokker–Planck equation for the r-evolution of the probability density
function (p.d.f.) of v(r). This equation for p(v, r) is completely determined by two
coefficients D1(v, r) and D2(v, r) (drift and diffusion coefficient, respectively). It is
shown how these coefficients can be estimated directly from the experimental data
without using any assumptions or models for the underlying stochastic process. The
solutions of the resulting Fokker–Planck equation are compared with experimentally
determined probability density functions. It is shown that the Fokker–Planck equation
describes the measured p.d.f.(s) correctly, including intermittency effects. Furthermore,
knowledge of the Fokker–Planck equation also allows the joint probability density of
N increments on N different scales p(v1, r1, …,
vN, rN) to be determined.
Pursuing security: economic resources and the ontological security of older New Zealanders
Authors: MANSVELT JULIANA , BREHENY MARY , STEPHENS CHRISTINE
Published: July 2013

Access to economic resources influences the material conditions of life for older people, as well as the freedoms and capacities of older people to achieve the kind of lives they value. Security is one aspect of later life valued by older people. Ontological security provides a sense of order and continuity and needs to be understood in terms of the situated life experiences and circumstances of older people. The study reported in this paper analysed 145 qualitative interviews with New Zealanders aged 63–93 in order to explore how participants understand ontological security. Varying levels of access to economic resources were associated with differing abilities of participants to manage the unpredictability of everyday life. Among the wealthy, security was strongly connected to the freedoms provided by ample financial resources. Contrary to what might be expected, those with the lowest levels of economic resources did not express higher levels of insecurity, but instead drew upon life experiences of managing and making do to construct a trajectory of security. Those with mid-range levels of economic resources expressed most insecurity, including anxiety over changing economic conditions and concerns over their ability to manage reductions in economic resources. In discussing the implications of this, the paper highlights the need to recognise ways in which access to economic resources intersect with life circumstances, past experiences and future social expectations to provide opportunities for all older people to pursue security as they strive to age well.
A cohomological splitting criterion for locally free sheaves on arithmetically Cohen–Macaulay surfaces
Authors: HALIC MIHAI , TAJAROD ROSHAN
Published: July 2013

In this paper we obtain a cohomological splitting criterion for locally free sheaves on arithmetically Cohen–Macaulay surfaces with cyclic Picard group, which is similar to Horrocks' splitting criterion for locally free sheaves on projective spaces. We also recover a duality property which identifies a generalK3 surface with a certain moduli space of stable sheaves on it, and obtain examples of stable, arithmetically Cohen–Macaulay, locally free sheaves of rank two on general surfaces of degree at least five in${\mathbb P}^3$.
SHOULD A FIRST-TRIMESTER RISK ASSESSMENT FOR PRE-ECLAMPSIA BE ROUTINELY OFFERED?
Authors: PARRA-CORDERO MAURO
Published: July 2013

From a scientific point of view, the answer to the question might be quite straightforward in favour of routinely screening all pregnant women for pre-eclampsia (PE) during the first trimester of pregnancy. However, irrespective of the large amount of good evidence and expert opinion favourable for universally screening for obstetric syndromes, such as PE, public health policies do not always align with pure clinical science.
The Influence of Age on Emotion Regulation Strategies and Psychological Distress
Authors: Brummer Laura , Stopa Lusia , Bucks Romola
Published: July 2013

Background:To date there is promising, yet limited, evidence to suggest that differences exist between older and younger adults’ emotion regulation styles.Aims:The study aimed to explore emotion regulation style across the adult lifespan by assessing whether self-reported reappraisal, or suppression, differs across age groups, and how these emotion regulation strategies may impact upon psychological distress.Method:Three hundred and seventeen younger, 175 middle-aged and 85 older adults’ emotion regulation styles and levels of psychological distress were measured using self-report questionnaires and examined using a cross-sectional design.Results:The findings suggest that, compared to younger adults, older adults make greater use of suppression, the emotion regulation strategy. This greater use of suppression by older adults was not related to increased levels of psychological distress. By contrast, younger adults who reported high levels of suppression reported higher levels of psychological distress. In addition, older adults reported less anxiety and stress than younger adults, with no age differences in depression.Conclusions:Findings suggest a possible decoupling of the use of emotional suppression and psychological distress with age. Suppression may be a useful form of emotion regulation for the stressors experienced in later life and, arguably, therefore may not be associated with the negative outcomes observed in younger adults.
Biodegradation Process of α-Tricalcium Phosphate and α-Tricalcium Phosphate Solid Solution BioceramicsIn Vivo: A Comparative Study
Authors: de Aza Piedad N. , Luklinska Zofia B. , de Val Jose E. Mate-Sanchez , Calvo-Guirado Jose L.
Published: July 2013

This article reports the structure and morphology of thein vivointerface between implants composed of either α tricalcium phosphate (αTCP) or αTCP doped with 3.0 wt% dicalcium silicate (αTCPss) ceramic, and natural bone of rabbit tibias. Both interfaces developed a new bone layer in direct contact with the implants after 4 and 8 weeks of implantation. The specimens were examined using analytical scanning and transmission electron microscopy, up to the lattice plane resolution level. Degradation processes of the implants developed at the interfaces encouraged osseous tissue ingrowth into the periphery of the material, changing the microstructure of the implants. The ionic exchange initiated at the implant interface with the environment was essential in the integration process of the implant, through a dissolution–precipitation–transformation mechanism. The interfaces developed normal biological and chemical activities and remained reactive over the 8-week period. Organized collagen fibrils were found at the αTCPss/bone interface after 4 weeks, whereas a collagen-free layer was present around the Si-free αTCP implants. These findings suggest that the incorporation of silicate ions into αTCP ceramic promotes processes of the bone remodeling at the bone/αTCPssinterface, hence the solubility rate of the αTCPssmaterial decreased.
Efficacy of agomelatine and escitalopram on depression, subjective sleep and emotional experiences in patients with major depressive disorder: a 24-wk randomized, controlled, double-blind trial
Authors: Corruble Emmanuelle , de Bodinat Christian , Belaïdi Carole , Goodwin Guy M.
Published: July 2013

In the present randomized, controlled, double-blind trial (12 wk treatment plus double-blind extension for 12 wk), 25–50 mg/d agomelatine (n = 164) and 10–20 mg/d escitalopram (n = 160) were compared for short- and long-term efficacy, subjective sleep and tolerability. The effects of these drugs on emotional experiences were also compared in patients having completed the Oxford Questionnaire on the Emotional Side-Effects of Antidepressants (agomelatine: n = 25; escitalopram: n = 20). Agomelatine and escitalopram similarly improved depressive symptoms, with clinically relevant score changes over 12 and 24 wk and notable percentage of remitters (week 12: 60.9 and 54.4%; week 24: 69.6 and 63.1% respectively). Over the 12 and 24-wk treatment periods, the ‘global satisfaction on sleep’ scores increased in both treatment groups and did not differ between groups. Satisfaction with sleep–wake quality was high in both groups; the ‘wellness feeling on waking’ was more improved with agomelatine than with escitalopram (p = 0.02). In patients with pronounced sleep complaints, quality of sleep and feeling on waking were significantly more improved with agomelatine than with escitalopram (p = 0.016 and p = 0.009, respectively). Emotional blunting was less frequent on agomelatine than on escitalopram. Indeed, 28% of patients on agomelatine vs. 60% on escitalopram felt that their emotions lacked intensity and 16% of patients on agomelatine vs. 53% on escitalopram felt that things that they cared about before illness did not seem important any more (p = 0.024). The tolerability profile of agomelatine was found to be superior to that of escitalopram and the incidence of patients with at least one emergent adverse event leading to treatment discontinuation was lower in the agomelatine group than in the escitalopram group (5.5 vs. 10.6%). The findings suggest that agomelatine displays additional long-term clinical benefits on sleep–wake quality and emotional experiences over escitalopram in the management of depression.
Inhibition of Soluble Epoxide Hydrolase after Cardiac Arrest/Cardiopulmonary Resuscitation Induces a Neuroprotective Phenotype in Activated Microglia and Improves Neuronal Survival
Authors: Wang Jianming , Fujiyoshi Tetsuhiro , Kosaka Yasuharu , Raybuck Jonathan D , Lattal K Matthew , Ikeda Mizuko , Herson Paco S , Koerner Ines P
Published: July 2013

Cardiac arrest (CA) causes hippocampal neuronal death that frequently leads to severe loss of memory function in survivors. No specific treatment is available to reduce neuronal death and improve functional outcome. The brain's inflammatory response to ischemia can exacerbate injury and provides a potential treatment target. We hypothesized that microglia are activated by CA and contribute to neuronal loss. We used a mouse model to determine whether pharmacologic inhibition of the proinflammatory microglial enzyme soluble epoxide hydrolase (sEH) after CA alters microglial activation and neuronal death. The sEH inhibitor 4-phenylchalcone oxide (4-PCO) was administered after successful cardiopulmonary resuscitation (CPR). The 4-PCO treatment significantly reduced neuronal death and improved memory function after CA/CPR. We found early activation of microglia and increased expression of inflammatory tumor necrosis factor (TNF)-α and interleukin (IL)-1β in the hippocampus after CA/CPR, which was unchanged after 4-PCO treatment, while expression of antiinflammatory IL-10 increased significantly. We conclude that sEH inhibition after CA/CPR can alter the transcription profile in activated microglia to selectively induce antiinflammatory and neuroprotective IL-10 and reduce subsequent neuronal death. Switching microglial gene expression toward a neuroprotective phenotype is a promising new therapeutic approach for ischemic brain injury.
Regenerative Glutamate Release by Presynaptic NMDA Receptors Contributes to Spreading Depression
Authors: Zhou Ning , Rungta Ravi L , Malik Aqsa , Han Huili , Wu Dong Chuan , MacVicar Brian A
Published: July 2013

Spreading depression (SD) is a slowly propagating neuronal depolarization that underlies certain neurologic conditions. The wave-like pattern of its propagation suggests that SD arises from an unusual form of neuronal communication. We used enzyme-based glutamate electrodes to show that during SD induced by transiently raising extracellular K+ concentrations ([K+]o) in rat brain slices, there was a rapid increase in the extracellular glutamate concentration that required vesicular exocytosis but unlike fast synaptic transmission, still occurred when voltage-gated sodium and calcium channels (VGSC and VGCC) were blocked. Instead, presynaptic N-methyl-D-aspartate (NMDA) receptors (NMDARs) were activated during SD and could generate substantial glutamate release to support regenerative glutamate release and propagating waves when VGSCs and VGCCs were blocked. In calcium-free solutions, high [K+]o still triggered SD-like waves and glutamate efflux. Under such a condition, glutamate release was blocked by mitochondrial Na+/Ca2+ exchanger inhibitors that likely blocked calcium release from mitochondria secondary to NMDA-induced Na+ influx. Therefore presynaptic NMDA receptor activation is sufficient for triggering vesicular glutamate release during SD via both calcium entry and release from mitochondria by mitochondrial Na+/Ca2+ exchanger. Our observations suggest that presynaptic NMDARs contribute to a cycle of glutamate-induced glutamate release that mediate high [K+]o-triggered SD.
Establishing Best Practices and Guidance in Population Modeling: An Experience With an Internal Population Pharmacokinetic Analysis Guidance
Authors: Byon W , Smith MK , Chan P , Tortorici MA , Riley S , Dai H , Dong J , Ruiz‐Garcia A , Sweeney K , Cronenberger C
Published: July 2013

This tutorial describes the development of a population pharmacokinetic (Pop PK) analysis guidance within Pfizer, which strives for improved consistency and efficiency, and a more systematic approach to model building. General recommendations from the Pfizer internal guidance and a suggested workflow for Pop PK model building are discussed. A description is also provided for mechanisms by which conflicting opinions were captured and resolved across the organization to arrive at the final guidance.

CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e51; doi:10.1038/psp.2013.26; advance online publication 3 July 2013
Identification of Post-Translational Modifications by Mass Spectrometry
Authors: Wetie Armand G. Ngounou , Sokolowska Izabela , Woods Alisa G. , Darie Costel C.
Published: June 2013

Proteins are the effector molecules of many cellular and biological processes and are thus very dynamic and flexible. Regulation of protein activity, structure, stability, and turnover is in part controlled by their post-translational modifications (PTMs). Common PTMs of proteins include phosphorylation, glycosylation, methylation, ubiquitination, acetylation, and oxidation. Understanding the biology of protein PTMs can help elucidate the mechanisms of many pathological conditions and provide opportunities for prevention, diagnostics, and treatment of these disorders. Prior to the era of proteomics, it was standard to use chemistry methods for the identification of protein modifications. With advancements in proteomic technologies, mass spectrometry has become the method of choice for the analysis of protein PTMs. In this brief review, we will highlight the biochemistry of PTMs with an emphasis on mass spectrometry.
Chemical Cross-linking and Mass Spectrometry for the Structural Analysis of Protein Assemblies
Authors: Calabrese Antonio N. , Pukala Tara L.
Published: June 2013

Cellular functions are performed and regulated at a molecular level by the coordinated action of intricate protein assemblies, and hence the study of protein folding, structure, and interactions is vital to the appreciation and understanding of complex biological problems. In the past decade, continued development of chemical cross-linking methodologies combined with mass spectrometry has seen this approach develop to enable detailed structural information to be elucidated for protein assemblies often intractable by traditional structural biology methods. In this review article, we describe recent advances in reagent design, cross-linking protocols, mass spectrometric analysis, and incorporation of cross-linking constraints into structural models, which are contributing to overcoming the intrinsic challenges of the cross-linking method. We also highlight pioneering applications of chemical cross-linking mass spectrometry approaches to the study of structure and function of protein assemblies.
Solid-phase peptide synthesis and solid-phase fragment coupling mediated by isonitriles
Authors: Wang Ting , Danishefsky Samuel J.
Published: July 2013

The synthesis of polypeptides on solid phase via mediation by isonitriles is described. The acyl donor is a thioacid, which presumably reacts with the isonitrile to generate a thio-formimidate carboxylate mixed anhydride intermediate. Applications of this chemistry to reiterative solid-phase peptide synthesis as well as solid-phase fragment coupling are described.
Methylation of the Protein Phosphatase 2A Catalytic Subunit Is Essential for Association of Bα Regulatory Subunit But Not SG2NA, Striatin, or Polyomavirus Middle Tumor Antigen
Authors: Yu Xing Xian , Du Xianxing , Moreno Carlos S. , Green Richard E. , Ogris Egon , Feng Qi , Chou Lisa , McQuoid Monica J. , Pallas David C.
Published: July 2013

Binding of different regulatory subunits and methylation of the catalytic (C) subunit carboxy-terminal leucine 309 are two important mechanisms by which protein phosphatase 2A (PP2A) can be regulated. In this study, both genetic and biochemical approaches were used to investigate regulation of regulatory subunit binding by C subunit methylation. Monoclonal antibodies selectively recognizing unmethylated C subunit were used to quantitate the methylation status of wild-type and mutant C subunits. Analysis of 13 C subunit mutants showed that both carboxy-terminal and active site residues are important for maintaining methylation in vivo. Severe impairment of methylation invariably led to a dramatic decrease in Bα subunit binding but not of striatin, SG2NA, or polyomavirus middle tumor antigen (MT) binding. In fact, most unmethylated C subunit mutants showed enhanced binding to striatin and SG2NA. Certain carboxy-terminal mutations decreased Bα subunit binding without greatly affecting methylation, indicating that Bα subunit binding is not required for a high steady-state level of C subunit methylation. Demethylation of PP2A in cell lysates with recombinant PP2A methylesterase greatly decreased the amount of C subunit that could be coimmunoprecipitated via the Bα subunit but not the amount that could be coimmunoprecipitated with Aα subunit or MT. When C subunit methylation levels were greatly reduced in vivo, Bα subunits were found complexed exclusively to methylated C subunits, whereas striatin and SG2NA in the same cells bound both methylated and unmethylated C subunits. Thus, C subunit methylation is critical for assembly of PP2A heterotrimers containing Bα subunit but not for formation of heterotrimers containing MT, striatin, or SG2NA. These findings suggest that methylation may be able to selectively regulate the association of certain regulatory subunits with the A/C heterodimer.
Adaptins
Authors: Boehm Markus , Bonifacino Juan S.
Published: July 2013

Adaptins are subunits of adaptor protein (AP) complexes involved in the formation of intracellular transport vesicles and in the selection of cargo for incorporation into the vesicles. In this article, we report the results of a survey for adaptins from sequenced genomes including those of man, mouse, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, the plant Arabidopsis thaliana, and the yeasts, Saccharomyces cerevisiae andSchizosaccharomyces pombe. We find that humans, mice, and Arabidopsis thaliana have four AP complexes (AP-1, AP-2, AP-3, and AP-4), whereas D. melanogaster,C. elegans, S. cerevisiae, and S. pombe have only three (AP-1, AP-2, and AP-3). Additional diversification of AP complexes arises from the existence of adaptin isoforms encoded by distinct genes or resulting from alternative splicing of mRNAs. We complete the assignment of adaptins to AP complexes and provide information on the chromosomal localization, exon-intron structure, and pseudogenes for the different adaptins. In addition, we discuss the structural and evolutionary relationships of the adaptins and the genetic analyses of their function. Finally, we extend our survey to adaptin-related proteins such as the GGAs and stonins, which contain domains homologous to the adaptins.
Activation of Matrix-Metalloproteinase-2 and Membrane-Type-1-Matrix-Metalloproteinase in Endothelial Cells and Induction of Vascular Permeability In Vivo by Human Immunodeficiency Virus-1 Tat Protein and Basic Fibroblast Growth Factor
Authors: Toschi Elena , Barillari Giovanni , Sgadari Cecilia , Bacigalupo Ilaria , Cereseto Anna , Carlei Davide , Palladino Clelia , Zietz Christian , Leone Patrizia , Stürzl Michael , Buttò Stefano , Cafaro Aurelio , Monini Paolo , Ensoli Barbara
Published: July 2013

Previous studies indicated that the Tat protein of human immunodeficiency virus type-1 (HIV-1) is a progression factor for Kaposi's sarcoma (KS). Specifically, extracellular Tat cooperates with basic fibroblast growth factor (bFGF) in promoting KS and endothelial cell growth and locomotion and in inducing KS-like lesions in vivo. Here we show that Tat and bFGF combined increase matrix-metalloproteinase-2 (MMP-2) secretion and activation in endothelial cells in an additive/synergistic manner. These effects are due to the activation of the membrane-type-1-matrix-metalloproteinase and to the induction of the membrane-bound tissue inhibitor of metalloproteinase-2 (TIMP-2) by Tat and bFGF combined, but also to Tat-mediated inhibition of both basal or bFGF-induced TIMP-1 and -2 secretion. Consistent with this, Tat and bFGF promote vascular permeability and edema in vivo that are blocked by a synthetic MMP inhibitor. Finally, high MMP-2 expression is detected in acquired immunodeficiency virus syndrome (AIDS)-KS lesions, and increased levels of MMP-2 are found in plasma from patients with AIDS-KS compared with HIV-uninfected individuals with classic KS, indicating that these mechanisms are operative in AIDS-KS. This suggests a novel pathway by which Tat can increase KS aggressiveness or induce vasculopathy in the setting of HIV-1 infection.
γ-Tubulin and the C-Terminal Motor Domain Kinesin-like Protein, KLPA, Function in the Establishment of Spindle Bipolarity inAspergillus nidulans
Authors: Prigozhina Natalie L. , Walker Richard A. , Oakley C. Elizabeth , Oakley Berl R.
Published: July 2013

Previous research has found that a γ-tubulin mutation inSchizosaccharomyces pombe is synthetically lethal with a deletion of the C-terminal motor domain kinesin-like protein genepkl1, but the lethality of the double mutant prevents a phenotypic analysis of the synthetic interaction. We have investigated interactions between klpA1, a deletion of an Aspergillus nidulans homolog of pkl1, and mutations in the mipA, γ-tubulin gene. We find that klpA1 dramatically increases the cold sensitivity and slightly reduces the growth rate at all temperatures, of threemipA alleles. In synchronized cells we find thatklpA1 causes a substantial but transient inhibition of the establishment of spindle bipolarity. At a restrictive temperature,mipAD123 causes a slight, transient inhibition of spindle bipolarity and a more significant inhibition of anaphase A. In the mipAD123/klpA1 strain, formation of bipolar spindles is more strongly inhibited than in theklpA1 single mutant and many spindles apparently never become bipolar. These results indicate, surprisingly, that γ-tubulin and the klpA kinesin have overlapping roles in the establishment of spindle bipolarity. We propose a model to account for these data.
A Novel Mechanism for Localizing Membrane Proteins to YeastTrans-Golgi Network Requires Function of Synaptojanin-like Protein
Authors: Ha Seon-Ah , Bunch Jeremy T. , Hama Hiroko , DeWald Daryll B. , Nothwehr Steven F.
Published: July 2013

Localization of resident membrane proteins to the yeasttrans-Golgi network (TGN) involves both their retrieval from a prevacuolar/endosomal compartment (PVC) and a “slow delivery” mechanism that inhibits their TGN-to-PVC transport. A screen for genes required for the slow delivery mechanism uncoveredINP53, a gene encoding a phosphoinositide phosphatase. A retrieval-defective model TGN protein, A(F→A)-ALP, was transported to the vacuole in inp53 mutants approximately threefold faster than in wild type. Inp53p appears to function in a process distinct from PVC retrieval because combining inp53 with mutations that block retrieval resulted in a much stronger phenotype than either mutation alone. In vps27 strains defective for both anterograde and retrograde transport out of the PVC, a loss of Inp53p function markedly accelerated the rate of transport of TGN residents A-ALP and Kex2p into the PVC. Inp53p function is cargo specific because a loss of Inp53p function had no effect on the rate of Vps10p transport to the PVC in vps27 cells. The rate of early secretory pathway transport appeared to be unaffected ininp53 mutants. Cell fractionation experiments suggested that Inp53p associates with Golgi or endosomal membranes. Taken together, these results suggest that a phosphoinositide signaling event regulates TGN-to-PVC transport of select cargo proteins.
RhoA-dependent Switch between α2β1 and α3β1 Integrins Is Induced by Laminin-5 during Early Stage of HT-29 Cell Differentiation
Authors: Gout Stéphanie P. , Jacquier-Sarlin Muriel R. , Rouard-Talbot Laurence , Rousselle Patricia , Block Marc R.
Published: July 2013

Integrin-mediated interactions between the basement membrane and epithelial cells control the differentiation of epithelia. We characterized the modulation of adhesive behaviors to basement membrane proteins and of integrin function in the human colon adenocarcinoma HT-29 cell line, which differentiates into enterocytes after the substitution of galactose for glucose in the medium. We demonstrate an increased capability of these cells to adhere to collagen type IV during the early stage of differentiation. This effect occurs without any changes in integrin cell surface expression but rather results from an α2β1/α3β1 integrin switch, α3β1 integrin becoming the major collagen receptor. The increase in laminin-5 secretion and deposit on the matrix is a key factor in the mechanism regulating cell adhesion, because it is responsible for the activation of α3β1 integrin. Furthermore, down-regulation of RhoA GTPase activity occurs during HT-29 cell differentiation and correlates with the activation of the integrin α3β1. Indeed, C3 transferase, a RhoA GTPase inhibitor, induces a similar α2β1/α3β1 switch in undifferentiated HT-29 cells. These results indicate that the decrease in RhoA activation is the biochemical mechanism underlying this integrin switch observed during cell differentiation. The physiological relevance of such modulation of integrin activity in the functioning of the crypt-villus axis is discussed.
Completion of Replication Map ofSaccharomyces cerevisiaeChromosome III
Authors: Poloumienko Arkadi , Dershowitz Ann , De Jitakshi , Newlon Carol S.
Published: July 2013

In Saccharomyces cerevisiae chromosomal DNA replication initiates at intervals of ∼40 kb and depends upon the activity of autonomously replicating sequence (ARS) elements. The identification of ARS elements and analysis of their function as chromosomal replication origins requires the use of functional assays because they are not sufficiently similar to identify by DNA sequence analysis. To complete the systematic identification of ARS elements onS. cerevisiae chromosome III, overlapping clones covering 140 kb of the right arm were tested for their ability to promote extrachromosomal maintenance of plasmids. Examination of chromosomal replication intermediates of each of the seven ARS elements identified revealed that their efficiencies of use as chromosomal replication origins varied widely, with four ARS elements active in ≤10% of cells in the population and two ARS elements active in ≥90% of the population. Together with our previous analysis of a 200-kb region of chromosome III, these data provide the first complete analysis of ARS elements and DNA replication origins on an entire eukaryotic chromosome.
Transforming Growth Factor β Enhances Epithelial Cell Survival via Akt-dependent Regulation of FKHRL1
Authors: Shin Incheol , Bakin Andrei V. , Rodeck Ulrich , Brunet Anne , Arteaga Carlos L.
Published: July 2013

The Forkhead family of transcription factors participates in the induction of death-related genes. In NMuMG and 4T1 mammary epithelial cells, transforming growth factor β (TGFβ) induced phosphorylation and cytoplasmic retention of the Forkhead factor FKHRL1, while reducing FHKRL1-dependent transcriptional activity. TGFβ-induced FKHRL1 phosphorylation and nuclear exclusion were inhibited by LY294002, an inhibitor of phosphatidylinositol-3 kinase. A triple mutant of FKHRL1, in which all three Akt phosphorylation sites have been mutated (TM-FKHRL1), did not translocate to the cytoplasm in response to TGFβ. In HaCaT keratinocytes, expression of dominant-negative Akt prevented TGFβ-induced 1) reduction of Forkhead-dependent transcription, 2) FKHRL1 phosphorylation, and 3) nuclear exclusion of FKRHL1. Forced expression of either wild-type (WT) or TM-FKHRL1, but not a FKHRL1 mutant with deletion of the transactivation domain, resulted in NMuMG mammary cell apoptosis. Evidence of nuclear fragmentation colocalized to cells with expression of WT- or TM-FKHRL1. The apoptotic effect of WT-FKHRL1 but not TM-FKHRL1 was prevented by exogenous TGFβ. Serum starvation-induced apoptosis was also inhibited by TGFβ in NMuMG and HaCaT cells. Finally, dominant-negative Akt abrogated the antiapoptotic effect of TGFβ. Taken together, these data suggest that TGFβ may play a role in epithelial cell survival via Akt-dependent regulation of FKHRL1.
The Target of Rapamycin Signaling Pathway Regulates mRNA Turnover in the YeastSaccharomyces cerevisiae
Authors: Albig Allan R. , Decker Carolyn J.
Published: July 2013

The target of rapamycin (TOR) signaling pathway is an important mechanism by which cell growth is regulated by nutrient availability in eukaryotes. We provide evidence that the TOR signaling pathway controls mRNA turnover in Saccharomyces cerevisiae. During nutrient limitation (diauxic shift) or after treatment with rapamycin (a specific inhibitor of TOR), multiple mRNAs were destabilized, whereas the decay of other mRNAs was unaffected. Our findings suggest that the regulation of mRNA decay by the TOR pathway may play a significant role in controlling gene expression in response to nutrient depletion. The inhibition of the TOR pathway accelerated the major mRNA decay mechanism in yeast, the deadenylation-dependent decapping pathway. Of the destabilized mRNAs, two different responses to rapamycin were observed. Some mRNAs were destabilized rapidly, while others were affected only after prolonged exposure. Our data suggest that the mRNAs that respond rapidly are destabilized because they have short poly(A) tails prematurely either as a result of rapid deadenylation or reduced polyadenylation. In contrast, the mRNAs that respond slowly are destabilized by rapid decapping. In summary, the control of mRNA turnover by the TOR pathway is complex in that it specifically regulates the decay of some mRNAs and not others and that it appears to control decay by multiple mechanisms.