X-ray diffraction of a gram-negative bacterial membrane mimetic

This thesis applies x-ray diffraction to measure he membrane structure of lipopolysaccharides and to develop a better model of a LPS bacterial melilbrane that can be used for biophysical research on antibiotics that attack cell membranes. \iVe ha'e Inodified the Physics department x-ray machine for use 3.'3 a thin film diffractometer, and have lesigned a new temperature and relative humidity controlled sample cell.\Ve tested the sample eel: by measuring the one-dimensional electron density profiles of bilayers of pope with 0%, 1%, 1G :VcJ, and 100% by weight lipo-polysaccharide from Pse'udo'lTwna aeTuginosa. Background VVe now know that traditional p,ntibiotics ,I,re losing their effectiveness against ever-evolving bacteria. This is because traditional antibiotic: work against specific targets within the bacterial cell, and with genetic mutations over time, themtibiotic no longer works. One possible solution are antimicrobial peptides. These are short proteins that are part of the immune systems of many animals, and some of them attack bacteria directly at the membrane of the cell, causing the bacterium to rupture and die. Since the membranes of most bacteria share common structural features, and these featuret, are unlikely to evolve very much, these peptides should effectively kill many types of bacteria wi Lhout much evolved resistance. But why do these peptides kill bacterial cel: '3 , but not the cells of the host animal? For gramnegative bacteria, the most likely reason is that t Ileir outer membrane is made of lipopolysaccharides (LPS), which is very different from an animal :;ell membrane. Up to now, what we knovv about how these peptides work was likely done with r !10spholipid models of animal cell membranes, and not with the more complex lipopolysa,echaricies, If we want to make better pepticies, ones that we can use to fight all types of infection, we need a more accurate molecular picture of how they \vork. This will hopefully be one step forward to the ( esign of better treatments for bacterial infections.

Cell wall degrading enzymes and interaction between Trichoderma Aggressivum and Agaricus Bisporus

Agaricus bisporus is the most commonly cultivated mushroom in North America and has a great economic value. Green mould is a serious disease of A. bisporus and causes major reductions in mushroom crop production. The causative agent of green mould disease in North America was identified as Trichoderma aggressivum f. aggressivum. Variations in the disease resistance have been shown in the different commercial mushroom strains. The purpose of this study is to continue investigations of the interactions between T. aggressivum and A. bisporus during the development of green mould disease. The main focus of the research was to study the roles of cell wall degrading enzymes in green mould disease resistance and pathogenesis. First, we tried to isolate and sequence the N-acetylglucosaminidase from A. bisporus to understand the defensive mechanism of mushroom against the disease. However, the lack of genomic and proteomic information of A. bisporus limited our efforts. Next, T. aggressivum cell wall degrading enzymes that are thought to attack Agaricus and mediate the disease development were examined. The three cell wall degrading enzymes genes, encoding endochitinase (ech42), glucanase (fJ-1,3 glucanase) and protease (prb 1), were isolated and sequenced from T. aggressivum f. aggressivum. The sequence data showed significant homology with the corresponding genes from other fungi including Trichoderma species. The transcription levels of the three T. aggressivum cell wall degrading enzymes were studied during the in vitro co-cultivation with A. bisporus using R T -qPCR. The transcription levels of the three genes were significantly upregulated compared to the solitary culture levels but were upregulated to a lesser extent in co-cultivation with a resistant strain of A. bisporus than with a sensitive strain. An Agrobacterium tumefaciens transformation system was developed for T. aggressivum and was used to transform three silencing plasmids to construct three new T. aggressivum phenotypes, each with a silenced cell wall degrading enzyme. The silencing efficiency was determined by RT-qPCR during the individual in vitro cocultivation of each of the new phenotypes with A. bisporus. The results showed that the expression of the three enzymes was significantly decreased during the in vitro cocultivation when compared with the wild type. The phenotypes were co-cultivated with A. bisporus on compost with monitoring the green mould disease progression. The data indicated that prbi and ech42 genes is more important in disease progression than the p- 1,3 glucanase gene. Finally, the present study emphasises the role of the three cell wall degrading enzymes in green mould disease infection and may provide a promising tool for disease management.

The Columbian Newspaper vol. IV no. 1105- June 12, 1813

The "Columbian" was established by Mr. Holt in 1808 as an "organ of the Clintonians" (Journalism in the United States, from 1690-1872 By Frederic Hudson) and a replacement to the "Citizen". It was a passionate Democratic paper that supported both Jefferson and Madison. Holt later sold the "Columbian" to Alden Spooner, who published the Long Island "Star". The Columbian ceased in 1821. This issue includes the following War of 1812 topics: Page 2: copies of letters from U.S. Gen. H. Dearborn describing the U.S. attack on Ft. George 27 May 1813; letter from Gen. H. Dearborn describing U.S. pursuit of British troops at Beaver Dams and the U.S. capture of Fort Erie; list of U.S. killed and wounded in Commodore Isaac Chauncey's squadron in attack on York 27 April, 1813; list of killed and wounded in Commodore Isaac Chauncey's squadron in attack on Ft. George 27 May 1813; abstract of the cartel for the exchange of prisoners of war between Great Britain and the United States; mention of troop movements through New York on their way to the battle front; list of persons killed or lost on the privateer Saratoga; Page 3: account of the loss of the U.S. war ships the Growler and Eagle to the British; news from Quebec and Kingston of troop movements; U.S. ship Syren unsuccessfully pursues British ship Herald; account of a U.S. cargo ship being captured by a British military ship; account of U.S. ship Siro capturing British ship Loyal Sam; report from Halifax of recent British troop and ship movements; list of recent troop enrollments in various states; report of British troop build up in Kingston;

Merrimack Intelligencer Vol. 5 No. 48

This was a weekly paper that was published every Saturday. The motto of the Merrimack was: "Not too rash--Yet not fearful--We aim to be just." It was published from 1808-1817. Topics of interest include: Page 1: State of New York Republicans published a statement arguing against the war and the policies of John Adams and James Madison; account of the capture of York by the Americans, 27 April 1813; Page 2: account of the capture of York by the Americans, 27 April 1813; letter from American Brig. Gen. Henry Miller to Sir John B. Warren warning the British not to execute captured U.S. citizen O'Neal; response from Sir John B. Warren to Brig. Gen. Henry Miller stating that O'Neal had been released; account of Stephen Girard buying back his ransomed ship from the British; Page 3: account of Stephen Girard buying back his ransomed ship from the British; U.S. General Harrison repels British and Indian forces that attack Fort Meigs; account of British forces capturing U.S. privateer ship Alexander; report of British forces near Newport, New York, the Delaware river, and the Potomac River; report of Indian attacks in Kaskaskia, Randolph County; report of a boat load of provisions attacked by Indians near Fort Harrison; Commodore Isaac Chauncey arrived at Sacket's Harbor to unload stores taken from York before leaving for Niagara to commence attack against Fort George; U.S. Army announcement recruiting men 18 to 45 years of age to enlist in the army;

Boston Patriot Vol. 8 No. 13- October 24, 1812

A semi-weekly paper that began in 1809 and ceased in 1816. Its succeeding title was the Boston Patriot and Morning Advertiser. Publishers included: Everett and Munroe, 1809-Mar. 7, 1810; Isaac Munroe, Mar. 10, 1810-May 1, 1811; Munroe and French, May 4, 1811-1813; D.C. Ballard, 1814-1816. Editor: David Everett, Mar. 10, 1810-Oct. 23, 1811. Topics of interest include: Page 1: announcement of war against Great Britain and the reasons for the war; Page 2: announcement of nomination of war supporter Francis Carr for Congress; Statement of the Senate of Massachusetts in support of the war; 3 accounts of the American attack on Queenston; Page 3: report of the movement of war ships in and out of the port of Boston; news of naval movements by American and British ships; Page 4: advertisement of American and British muskets and swords for sale;

The New York Weekly Museum Newspaper, Vol. II, No.25- October 23, 1813

A weekly paper that was published from 1805 to 1814. War related news includes: Page 99 - Weekly Retrospect: American report on British naval movements near Louisiana; General William Harrison reports on: a victory at Moravian Town (Moraviantown) on October 5; Ottawas, Chippewas, Wyandots Miamies and Delaware First Nations (Indians) leaving the British side; Tecumseh remaining with the British; American army and navy attempt for a reduction of Mackinac and St. Joseph's; Colonel Chapin attacking a British picket guard near Fort George on October 6; Report that the British have abandoned the Fort George area for Kingston and is being pursued by General McClure; Forces in Sackett's Harbour ready for an attach on Canada; General Provost believed to have left Kingston for Montreal with 1000 men; Report from Burlington (Lake Champlain) of an attack on St. Armands against Colonel Clark on October 15; Report of the American's taking of the Packet Morgiana by the Schooner Saratoga under Captain Adderton by Newport; Announcement by the New York City Common Council for a celebration of Perry and Harrison's victories on the evening of October 23. The rest of the newspaper contains literary works (poems and translations), marriages, deaths and other anecdotes. The motto on the front page states: "Visiting Every Flower with Labour Meet, and Gathering all its Treasures, Sweet by Sweet."

The New York Weekly Museum Newspaper, Vol. II, No.26- October 30, 1813

A weekly paper that was published from 1805 to 1814. War related news includes: Page 103 - Weekly Retrospect: Reports on the Napoleanic Wars in Europe; Possible French and English troop movements from Europe to America and Canada; Mention of British vessels captured by American privateers Scourge, Rattlesnake and Lion; Report on New York celebration of Commodore Perry and General Harrison's victories on Lake Erie and in Canada respectively; Creek Indians attack on a supply convoy near Savannah, the provisions were recovered by General Floyd; General Harrison's account on Moravian Town (Moraviantown) and Munsey; Movements of General Wilkinson's army. Page 104 - an editorial about the madness of the times and its reflection on humanity. The rest of the newspaper contains literary works (poems and translations), marriages, deaths and other anecdotes. The motto on the front page states: "Visiting Every Flower with Labour Meet, and Gathering all its Treasures, Sweet by Sweet."

Independent Chronicle Vol. XLVI No. 2476- August 4, 1814

A semi-weekly paper that was published from 1801 to 1817. It was previously called the Independent chronicle and the universal advertiser, and was later the Independent chronicle and Boston patriot (Semiweekly). Publishers were Abijah Adams and Ebenezer Rhoades. Topics of interest in this issue include: Page 1: Proclamation from James Madison pardoning military deserters if they return to military service; announcement to officers and soldiers in the military offering reward for the return of military deserters; U.S. General W. Scott's account of the battle of Chippewa; U.S. General P. B. Porter's account of the battle of Chippewa; Major J. Hindman's account of the battle of Chippewa; news of British war ships attacking and capturing U.S. cargo ships; Page 2: news of a soldier shot for desertion; military news from Erie, Pennsylvania; New York appropriates money to pay troops and build two encampments; James Madison issues orders for state of Rhode Island to raise a militia of 500 troops; U.S. military news from Bermuda; report of the death of Capt. Parker of the U.S. ship Syren; account of the battle of Chippewa and a list of important officers wounded; report of a raft captured that was taking supplies to the British; report of U.S. General Brown being wounded in battle; list of further details of the battle of Chippewa; report of Indian attack near Champlain; news of prisoner exchange and announcement that exchanged prisoners should return to their regiments; listing of the total number of British forces in the U.S.; report of British shipwrecks; Naval news for the Port of Boston; news of various U.S. war ships; Page 4: Marshal's notice announcing a trial for members of a private American ship accused of supplying the British with provisions;

Independent Chronicle Vol. XLVI No. 3477- August 8, 1814

A semi-weekly paper that was published from 1801 to 1817. It was previously called the Independent chronicle and the universal advertiser, and was later the Independent chronicle and Boston patriot (Semiweekly). Publishers were Abijah Adams and Ebenezer Rhoades. Topics of interest in this issue include: Page 1: notice from the U.S. War Department seeking proposals for the supply of rations to troops; account of the battle of Bridgewater; list of important military figures wounded in the battle; news of prisoner exchange; Americans and the British negotiate and new prisoner exchange convention; Page 2: report of more British troops sailing to North America; report of some Indian tribes signing a treaty to fight against the British; report of battle near Detroit; report of militia moving from Fredricksburg, Virginia to Baltimore, Maryland; report of troop numbers and casualties in the battle of Bridgewater; report that Commodore Chauncey has recovered from his illness; news of American Naval forces sailing from Sackett's Harbor; Indian tribes sign peace treaty with U.S.; news of U.S. relations with Indians in the southern U.S.; account of battle of Bridgewater and list of casualties; report of the number of men killed and wounded on both sides in the battle of Chippewa; Page 3: report of surprise attack on the British; news of warship movements in and out of Halifax; frigate Java launched in Baltimore; news of British ship movements; 3 companies of Massachusetts militia arrive at Fort Warren; news of ship movements in and out of the Port of Boston; various Marshal's notices alleging U.S. ships supplying goods to the British;

Independent Chronicle Vol. XLVI No. 3470- July 14, 1814

A semi-weekly paper that was published from 1801 to 1817. It was previously called the Independent chronicle and the universal advertiser, and was later the Independent chronicle and Boston patriot (Semiweekly). Publishers were Abijah Adams and Ebenezer Rhoades. Topics of interest in this issue include: Page 1: report of Independence Day celebration including multiple toasts to the military; Page 2: report of South Carolina militia marching home; report of U.S. schooner Alligator being lost to a tornado in Port Royal; report of 10,000 militia and 2,000 regular Army troops to be used in defense of the District of Columbia and vicinity; report U.S. is to try to raise 100,000 militia for defense; news of British deserters providing information to the U.S.; report of skirmishes along the U.S. coast; statement from U.S. Navy Capt. David Porter stating he had taken possession of Sir Henry Martin's Island; report of British troops burning a militia barracks in Lewiston, N.Y.; 4 accounts of the battle of Chippewa and the taking of Fort Erie; statement from Maj. Gen. Brown in praise of his troops in the battle of Chippewa; copy of General Brown's orders to attack at Fort Erie; essay arguing against U.S. citizens boarding enemy ships; report of peace treaty rumours; Page 3: account of Capt. Porter's capture and subsequent escape from the British; list of American prisoners held on the British ship Nymph; report of British cargo ship captured by U.S. war ship; Proclamation from James Madison pardoning military deserters if they return to military service; announcement to officers and soldiers in the military offering reward for the return of military deserters; Page 4: 2 reward advertisements for return of military deserters;

Correspondence between Mr. Monroe and Mr. Canning and between Mr. Madison and Mr. Rose

Full Title: Report of the Committee to whom was Referred the Correspondence between Mr. Monroe and Mr. Canning, and between Mr. Madison and Mr. Rose, relative to the attack on the Chesapeake : and also a communication from the President of the United States of the 30 March last, with a letter from Mr. Erskine to the Secretary of State, and a letter from M. Champagny to Gen. Armstrong Printed by R. C. Weightman

A View of the Fort and Harbour of Oswego from Lake Ontario, from the American Magazine March 1816

An image within the American Magazine, March 1816 Vol. I, No. 10. Page 369. A View of the Fort and Harbour of Oswego from Lake Ontario. Below the image it reads: "T. H. Wentworth del." Below the title it reads: "Representing the Attack by the British on the 6th of May 1814" Conducted by Horatio Gates Spafford, A.M. F.A.A.

Letter written by John Bentley, Sept. 26, 1813.

Transcript [original spelling and grammar retained]: Sacketts Harbour 26th Sept. 1813. Dear wife. From this you are informed that I am in health at this Date. When I last wrote to you I some expected to go upon and expedition but to us unknown we sat out and went up the Lake 3 Days Landed at Oswego The British Fleet appeared off, and we returned and saw our fleet upon our return, I think that our Regt. going was only a maneuver to get the Fleet out that our Fleet might come a threat[?] of them We expect to embark immediately into Canada as preparations are making to convey us over to them we are anxious to commence an action with them. Troops are daily coming in to the Harbour to take the Stand in our absence, we shall not be here 3 days before we try their[?] Powder. they are daily defecting[?] to us from Canada very fearful of the consequence of our Resisting[?] of them…our Fleet is now out and has been for 6 or 7 days. The Lake Erie fleet has done great things. I hope ours will be as successful. I think that our Generals are waiting to hear from them as every thing is ready[?] of to embark various opinions reflecting were we shall attack them some say at Kingston others at Montreal and others at Prescot—Mr. William Butler and D[?]…are well and in Spirits, Sergt Daniel White is very hearty for him, M. Samuel C[?] is well and in good health Benjm Thompson is well Charles Bryant is well [?] is well Eben[?] Smith is very much plagued with the Rheumatik Disease[?] he……… his limbs very often for being Crippled[?] he is at the Hospital I often visit it to see the sick Jacob Barnes is at the Hospital but recovering fast been very sick. Luther Gregory is at the Hospital and on the recovery, Sergt. L[?] & Smith are well, Henry ………[?] is well, very healthy have not more die here than 3…[?]to the best of my knowledge. I will make a few remarks upon the place it abounds in Lime Rock more than Thomaston and not every person to my knowledge burn it, and in the whole Town not but one Pump that supplies the Towns People and Soldiers and a ………[?] of such a Lake of water the Lake water is good for drinking but the water near the Shore is exposed to all kind of filth being thrown into it. The officers with whom I have been with have used me kindly and I get quietly by them. The Lieut. Downer who recruits at Thomaston tell me he has thots[?] of Leaving the army if so I must say I am greatly sorry as he was my ……[?] friend although he Left us and went in a northern Company it is a Company……………[?]worthy an officer as he proves to be, I cannot get any higher than a Sergeant or Quarter Master Sergeant which I may have without any friends at Thomaston assisting me. I am a Sergeant and Sergeant Daniel White is expecting[?] to be a Quarter Master Sergeant, and a number of his friends from Thomaston have went to their Major for him in the 9th Regt Major….[?] and he expects to obtain a Commission as I ……[?] expect to be promoted and it died away he will have the Laugh upon me, I wish that My Friend Dawes would[?] put the question to Col. Foot? to write to our Col. E.W. Ripley if he has …[?]in the …[?]taken by him and others of my …[?] friends[?]. I expect to come home this winter without fail. I remain your Loving Husband till Death. John Bentley for Betsey Bentley Thomaston P.S. The next Letter will be ……[?]to Mr. Dawes[?] and shall write as soon as our Fleet arrives or if we are ordered off tomorrow shall write before I leave this Place. I have understood that many letters have been ……[?]to me. I have received only 2 from Mary, one from Mr. Dawes, one from William Thompson and have answered them please to write……[?]to S. Harbour.

Letter from J.E.A. Masters to Josiah Masters, November 11, 1812

Transcription: Encampment Plattsburgh My Dear Uncle Nov. 11th 1812 We are making every possible preparation to invade Canada. I have no doubt but we march in six days. From the best information I can get it is not contemplated to attack the Isle aux Noix – We shall take into the field 2500 infantry between 3 & 4 hundred cavalry 25 light artillery & 150 artillerists; of the malitia I have no accurate knowledge there is more than 1000 of them, the number of regular troops is mentioned you may rely on as being nearly correct I cannot state to a man as I have not had an opportunity of being the consolidated returns of the different corps. It is said that a [corps formed?] of volunteers are to join us from Vermont. I think it doubtful I believe that we shall have no great difficulty in going to Montreal as to the ultimate policy of the [act it is?] not my duty to judge. Confidential our troops are raw particularly in loading and firing they are much deficient. The 6th and 15th will be able to act with some considerable ... of precision and accuracy the remaining infantry—badly disciplined. Should any thing [occur?] with me my fate be unfortunate the [little?] property willed me by my grandfather will secure you the amount I owe you. General Dearborn I understand is at Burlington on his way here. Some of the prisoners that were taken at Queenstown have [arrived?] at Montreal probably. [Ensign Rich?] is among them. Several officers here became acquainted with him soon after he received his [two illegible words] & speak highly of him. [Always?] affectionately yours J. E. A. Masters P.S. I shall write you again before we march excuse this [scrawl?] my hand are too cold to write a fair hand we shall have here near [400?] sick that are not able to march J. E. A. Masters The [Hon.?] Josiah Masters [Schaghticoke?] N.Y. N. B. Nov. 13th We have orders to be prepared to march on the 15th at 12 oclock. Our baggage will be contained as much as possible. The officers carry no baggage except what they carry in their knapsacks. I am in fine health and am able [Hand?] most any [illegible word] My love to all affectionately Your nephew J. E. A. Masters

Daniel D. Tompkins letter to General Dearborn, June 28, 1812.

Transcript [original spelling and grammar retained]: Albany June 28 1812 Sir Your letter of the 23d has been received. I had anticipated your request by ordering the detachment from Washington, Essex, Clinton and Franklin Counties into service and have fixed the days and places of their Rendezvous. Upon application to the quarter master General I find there are but 139 tents & 60 camp kettles at this place & even those I take by a kind of stealth. The Deputy Quarter Master General declines giving an order for their delivery until he shall have a written order from the Quarter Master General, and the latter is willing I Shall take them but will not give the Deputy a written order for that purpose. Under Such circumstances I shall avail myself of the rule of Possession and by virtue of the Eleven Points of Law Send them tomorrow morning without a written order from anyone. You may remember that when you were Secretary of the war department I invited you to forward and deposit in our Frontier Arsenals, arms ammunition and camp equipage free of expense to be ready in case of war and the same invitation to the war department has been repeated some time, Since The United States have now from 5 to 600 regular troops at Plattsburgh, Rome, Canandaigua & c, where those arsenals are, and yet those recruits are now and must be for weeks to come unarmed and unequipped in every respect although within musket Shot of arsenals. The recruits at Plattsburgh are within 50 miles of two tribes of Canadian Indians. In case of an attack upon the Frontiers that portion of the United States army would be as inefficient and unable to defend the inhabitants or themselves even. The Militia Detachments on the Western Frontiers received the news of war with [cherafulness] and determined courage, and I am happy to find they are united late brothers, highly improved in Discipline & ready to devote themselves to any Service or danger which the good of the Country may require. But they are in barracks from which they cannot move a days march for the want of tents and other equipage, and they are in Separate and Independent Detachments without a General Officer to command them or combine their exertions for the accomplishment of any desirable and important object. The only officer of the United States here who can do anything is the Quarter Master General and he has not a tent Camp Kettle or Knapsack in this arsenal except what I have concluded to send off tomorrow morning as above mentioned to furnish men As to Cannon Muskets and Ammunition. I can find now one here who will exercise any authority over them or deliver a Single article upon my requisition. Neither can I find any Officer of the army who feel himself authorized to exercise any authority or do any act which will aid me in the all important object of protecting the Inhabitants of an extended Frontier exposed to the Cruelties of Savages and the depredations of the enemy. If I must rely upon the Militia Solely for Such protection I entreat you to give orders to your Officers to furnish upon my orders, for the use of the Militia Detachments , all needful weapons and articles with which the United States are Supplied and of which we are destitute . You may rely upon all the assistance which my talents, influence or authority can furnish in the active prosecution of the first & necessary way which has been declared by the Constituted Authorities of our beloved Country. I am, Sir, respectfully Your ob. Servt. Daniel D. Tompkins