<?xml version="1.0"?>
<api>
  <query-continue>
    <allpages gapcontinue="Sandbox" />
  </query-continue>
  <query>
    <pages>
      <page pageid="140" ns="0" title="Recipes">
        <revisions>
          <rev contentformat="text/x-wiki" contentmodel="wikitext" xml:space="preserve">==C==
===Coppe di amaretti, castagne e mascarpone===
* Castagne lesse 350 gr
* Cioccolato fondente 120 gr
* Mascarpone 250 gr
* Vanillina 1 bustina (facoltativo)
* Amaretti q.b.
* Liquore (nocino o amaretto) 1 bicchierino
* Zucchero a velo 100 gr
* Latte q.b. (v.sotto)
* Burro 50 gr (facoltativo)

Frullare le castagne lessate in un mixer, aggiungendo un poco di latte per rendere l'operazione più facile se necessario. Aggiungete il bicchiere di liquore, il mascarpone, la vanillina e lo zucchero a velo, e frullare nuovamente.

Sciogliere il cioccolato fondente a bagnomaria (col burro se si desidera, io ho fatto senza) e aggiungerlo alla crema. Amalgamare con un cucchiaio o di nuovo col mixer. Versare in coppette e sbriciolare gli amaretti sopra. Servire subito o conservare in frigo.

==F==

===Focaccia genovese===
Per la pasta:

* 160 gr. di acqua
* 300 gr. di Farina 00
* 1 cucchiajo di olio extravergine d’oliva
* 14 gr. di lievito di birra
* 1 cucchiaino da the di sale

Per l’emulsione:

* 3 cucchiai di olio extravergine d’oliva
* 3 cucchiai di d’acqua
* 1/2 cucchiaino da the di sale

Mettere nella ciotola la farina, versare il lievito sciolto nell’acqua tiepida e l’olio, impastare, quando inizia a formarsi l’impasto unire il sale; lasciar lievitare coperto (con pellicola e un burazzo) per circa 45 minuti.

Ungere una teglia da 26 cm di diametro con olio, stendere la focaccia e affondare le dita per creare dei buchi, battere olio, acqua e sale per formare l’emulsione, versarla sulla focaccia, distribuirla bene rifacendo i buchi.

Lasciar lievitare coperto per ancora 30/45 minuti; infornare a 250 C per 10/15 minuti (io cuocio a 200 per circa 18-20 min), sfornare e togliere subito dalla teglia altrimenti inumidisce.

==G==

===Ginger beer/soda, homemade===

Adapted from a recipe by Jean-Georges Vongerichten (famous chef in the US)

Ingredients:

For the syrup:

* 1 pound fresh ginger, unpeeled and cut into small dice
* optional) 2 stalks lemongrass, trimmed and roughly chopped
* 2 small fresh (I used dried) chiles
* 1 1/2 cups sugar (1 cup = 240 mL)

To serve:

* Soda water
* Lemon or Lime 

Place everything (except the soda water and lemon/lime wedges) in a pot with four cups of water (~1 liter), bring to the boil, reduce to a simmer for about 15-20 minutes. Let it cool completely. Strain out the solids, and refrigerate. You now have the syrup to use to make the soda.

To serve, use about 1/4 a cup (say, a finger in a normal water glass), fill the rest of the glass with sparkling water, squeeze 1/4 lemon or lime, could also add ice. 

(''thanks to Shoshana Goldsten'')

==P==

===Pancakes===
* 110g/4oz plain flour, sifted
* pinch of salt
* 2 eggs
* 300 ml fresh whole milk
* 50g/2oz butter
* (optional) some leavening powder

Mix the eggs, flour and salt together with a fork. When homogenous, start adding the milk, slowly, continuing to mix. When all the milk has been added, put the butter in a pan and let it melt. Pour the melted butter in the batter, leving just a bit in the pan. Pour a ladle or two of batter in the hot pan, turning once.

===Pollo alla Watchmen===

Per ciascuno (abbondante):
* 1 scaloppina di pollo
* 1/2 barattolo di olive
* 1 indivia belga un po' grande o 2 piccoline
* 2 fette di taleggio
* olio

Scaldare un po' d'olio in padella, aggiungere le olive tagliate a pezzetti non troppo fini e l'indivia belga tagliata in senso orizzontale (ad anelli, non per il lungo). Passare il tutto in padella qualche minuto fino a quando l'indivia non ammorbidisce un po'. Aggiungere il pollo e il formaggio, e cuocere a fuoco medio-basso mescolando frequentemente; verso la fine aggiungere un pizzico di sale.

==R==

===Ragù===
x 2 persone

* almeno 2 hg carne macinata
* 1/2 cipolla grossa o 1 cipolla piccola
* sedano 
* 1 carota
* aglio
* vino rosso (opz.)
* un poco di polpa di pomodoro
* erbe

tritare le verdure finemente. mettere in un tegame/pentolino con un po' d'olio e si fanno rosolare. 

prima che incomincino a bruciare si butta la carne, si rosola mescolando continuamente e facendola cuocere.

aggiungere 1 o 2 dita di vino rosso e si lascia sfumare.

aggiungi il pomodoro e 1 bicchiere di acqua.

si porta a ebollizione e si cuoce coperto a fuoco lentissimo per almeno 1h30' o anche più, aggiungendo acqua e aggiustando sale ed erbette aromatiche. controllare che non si attacchi e che l'ebollizione sia bassa.


==S==

===Shoshana's baked eggs with greens===

* 3 endives, sliced
* 1 white onion, minced
* 1 clove garlic, minced
* 4 cubes, frozen spinach
* 3-4 eggs
* butter, olive oil
* white wine
* 1/2 lemon
* peperoncino flakes
* herbs (whatever you have on hand, but I used thyme, sage, parsley)

Heat a tab of butter and some olive oil in a saute pan. Add onion, garlic, a pinch of salt, the herbs, and cook until the onions become translucent, or slightly caramelized. Add the endive, spinach, a few more pinches of salt, peperoncino flakes, and continue to cook until the endive is wilted, cooked through. Add a little (a finger or so) of wine, juice of half a lemon, and continue cooking. Taste-test for flavor, add salt etc. depending. Transfer to ovenproof dish. Create small wells in the cooked veggies and gently crack the eggs into the wells. Bake around 175 for 10-15 minutes. Egg yolks should be slightly runny or soft boiled. Could serve with grated cheese, yogurt or tahini as a toppings if desired. 

===Shoshana's pseudo Moroccan chicken tajine recipe===

* 3 cloves garlic, peeled and finely chopped
* red chili flakes (as desired)
* 1/2 teaspoon ground cumin
* 1/2 teaspoon ground ginger
* 1/4 teaspoon sweet paprika
* 1/2 tablespoon salt
* 1/4 teaspoon freshly ground black pepper
* 1 large onion, grated or finely chopped
* 2 tablespoons olive oil
* 1 to 2 preserved or fresh lemons
* 4-5 chicken thighs, with bone and skin
* Stems from the parsley and cilantro
* 1/4 teaspoon powdered saffron or 1/4 teaspoon powdered turmeric 
* 1 cup pitted green olives
* 1/2 bunch Italian parsley, about 1/4 cup chopped
* 1/2 bunch cilantro, about 1/4 cup chopped


In a large bowl, mix the garlic, cumin, ginger, paprika, salt and pepper, chili, 1/2 grated onion, and the oil.
Add lemon pulp. Put aside the lemon peel for later use.
Add the chicken. Mix everything together and place to marinate for several hours, overnight is even better, in the refrigerator. (Twenty-four hours really gives the chicken the best flavor.)

In a large Dutch oven or casserole, place the chicken and marinade; add the stems of the parsley and cilantro, the rest of the grated onion, lemon shells, the powdered saffron and 2 cups water. Bring to a boil over high heat, turn down to a simmer and cook, partially covered, for 30 minutes. 
Remove the cover, stir the chicken and continue to simmer for another 15 minutes or.
Remove the chicken to a serving dish and cover with foil to keep warm. Keep sauce on stove and begin to reduce.
Add the olives, parsley and cilantro. Reduce until the sauce is just a little thick. 
Uncover the chicken and remove the skin from the chicken. Pour sauce over chicken and serve with couscous.

The leftover broth is good for soup

{{food}}
[[Category:Food]]</rev>
        </revisions>
      </page>
      <page pageid="52" ns="0" title="Research">
        <revisions>
          <rev contentformat="text/x-wiki" contentmodel="wikitext" xml:space="preserve">{{in progress}}

During my research career, I have been involved in quite different aspects of '''protein biophysics'''. My path has been relatively ecletic, but with a definite ''trait d'union'': understanding proteins as dynamical chamaleontic systems which can populate lots of dramatically different structures. 

==Single molecule AFM force spectroscopy==

===General reviews===
* Sandal M., Zuccheri G., Samori B. 
:''Inside the small length and energy scales of the world of the individual biological molecule'', 
:in &quot;From cells to proteins: Imaging Nature across dimensions&quot;, pp.111-137, Springer, 2005 
:([http://www.springerlink.com/content/f54n3531011l1180/ DOI: 10.1007/1-4020-3616-7_7])

* Valle F., Sandal M., Samorì B. ''The interplay between chemistry and mechanics in the transduction of a mechanical signal into a biochemical function'' 
:Physics Of Life Reviews 2007, 4(3) 
:([http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B75DC-4P7FSFW-1&amp;_user=10&amp;_coverDate=09%2F30%2F2007&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_rerunOrigin=scholar.google&amp;_acct=C000050221&amp;_version=1&amp;_urlVersion=0&amp;_userid=10&amp;md5=6416722571a32f1ebf0d472b8ac88af6&amp;searchtype=a  doi:10.1016/j.plrev.2007.06.001])  
:('''free arXiv preprint''':[http://arxiv.org/pdf/0705.2706  q-bio/0705.2706])

Two generic reviews about the application single molecule force spectroscopy on proteins and the recent insights on mechanochemistry in biology.

===Relationship between mechanical and redox switches in {{en|angiostatin}}===

*Sandal M., Grandi F., Samorì B. 
:''Single molecule force spectroscopy discovers mechanochemical switches in biology: the case of the disulfide bond'' 
:Polymer 47 (7): 2571-2579, 2006 
:([http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6TXW-4J90W56-1&amp;_user=10&amp;_coverDate=03%2F22%2F2006&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_rerunOrigin=scholar.google&amp;_acct=C000050221&amp;_version=1&amp;_urlVersion=0&amp;_userid=10&amp;md5=488e8d2a6b6726eada66d14b39b8f304&amp;searchtype=a doi:10.1016/j.polymer.2005.12.084 ])

*Grandi F.#, Sandal M.# Guarguaglini G., Capriotti E., Casadio R., Samorì B. 
:''Hierarchical mechanochemical switches in Angiostatin''
: ChemBioChem 2006, 7,1774-1782 (#=shared first) 
:([http://onlinelibrary.wiley.com/doi/10.1002/cbic.200600227/full DOI: 10.1002/cbic.200600227])

In my initial research work, planned and started as an undergraduate, I revealed the presence of mechanical unfolding intermediates in the protein angiostatin, and associated to its disulfide redox state regulation by thioredoxin. The study suggested a novel cell signalling pathway that emerges from the integration of disulfide redox switches and cell migration mechanical forces. The work unveiled how out of equilibrium structures induced by mechanical forces could be of functional interest also for proteins not directly involved in muscle mechanics.

===Conformational ensembles of amyloidogenic proteins at the single molecule level===

* Sandal M.#, Valle F.#, Tessari I., Mammi S., Bergantino E., Musiani F., Brucale M., Bubacco L., Samorì B. 
:''Conformational Equilibria in Monomeric Alpha-Synuclein at the Single Molecule Level''
:PLoS Biology 2008 6(1):e6  (#=shared first) 
:('''free open access''': [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060006 doi:10.1371/journal.pbio.0060006]) ('''free arXiv preprint''': [http://arxiv.org/pdf/0712.1973v1 q-bio:0712.1973])

* Brucale M. , Sandal M. , Di Maio S., Rampioni A., Tessari I., Bubacco L., Samorì B.
: ''Pathogenic Mutations Shift the Equilibria of alpha-Synuclein Single Molecules towards Structured Conformers''
: ChemBioChem 2009  Jan 5;10(1):176-83.

* Sorce B., Sabella S., Sandal M., Samorì B., Santino A., Cingolani R., Rinaldi R., Pompa P.P. 
:''Single-Molecule Mechanical Unfolding of Amyloidogenic beta(2)-Microglobulin: The Force-Spectroscopy Approach.''
: ChemPhysChem 2009 Jun 3

* Sandal M. , Brucale M. , Samorì B. 
:''Monitoring the conformational equilibria of monomeric intrinsically disordered proteins by single molecule force spectroscopy'' 
:in &quot;Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure  and  Conformation&quot; , edited by Uversky and Longhi , pp. 391-432, John Wiley and Sons. , 2009 

I moved towards the experimental determination of the conformational ensembles that proteins populate at equilibrium, focusing on proteins prone to aggregation. I reported the first measurements of an intrinsically unstructured protein ({{en|alpha-synuclein}}) conformational equilibria by means of single-molecule force spectroscopy. We reported that shifts in the population of one of the conformational basins are linked to the protein aggregation propensity. The approach that I developed has been recognized as a promising methodology to the  study of unstructured proteins. The initial results that we obtained have been further validated by the study of naturally occuring pathogenic variants of alpha-synuclein and to the native-like aggregation of beta-2-microglobulin.

===Single molecule force spectroscopy data analysis===
* Sandal M., Benedetti F., Brucale M., Gomez-Casado A., Samorì B. 
:''Hooke: an open software platform for force spectroscopy''
:Bioinformatics 2009 Jun 1;25(11):1428-30. Epub 2009 Mar 31 
: [http://code.google.com/p/hooke Software website]

I independentely conceived and designed and implemented what has become the de facto standard data analysis application of my own research group, one of the first open source tools for single molecule force spectroscopy.  The software has a modular structure which allows for easy extension of its capabilities by users. Currently I am extending the software to include automatic clustering of force curves (Pancaldi P. , Samori` B., Sandal M., manuscript in preparation). It is now used by several other research groups and it is under continous development by an international team. This was the first move for my laboratory into development of data analysis tool and techniques, effectively opening a whole new research avenue in my Bologna laboratory which is now being pursued by students and has led to further publications after I left the group.

==Single molecule FRET studies of alpha-synuclein oligomerization==
* Cremades N., Chen A.Y. , Orte A., Sandal M., Clarke R., Klenerman D. and Dobson C.M.
(manuscript in preparation)

==Coarse grained models for protein folding and aggregation==
Sandal M. and Vendruscolo M.
(current work)

I have developed a version of the tube model for the molecular dynamics package GROMACS to investigate protein aggregation. Current results seem to explain the bewildering oligomerization diversity observed in experimental investigations of early aggregation processes.


{{personal}}
[[Category:Personal]]</rev>
        </revisions>
      </page>
    </pages>
  </query>
</api>