Iyer Laboratory Solid Tissue Chromatin Immunoprecipitation Protocol

A detailed protocol on how to perform chromatin immunoprecipitation in solid tissue samples. This protocol is used routinely in the Iyer lab.Molecular Bioscience

Iyer Laboratory: Gel-free Library Preparation Protocol

Originally developed by Amelia Weber Hall in October 2012, then modified to avoid usage of silica gel columns to improve yield. Used for preparing libraries of DNA derived from chromatin immunoprecipitation experiments by the Iyer lab, and distributed to several other labs across Central Texas. Documented by Amelia Weber Hall, December 2012, March 2015, and June 2017. This protocol should work well with any DNA that needs to be prepared into a library for high-throughput sequencing, however it is highly optimized for small (nanogram to pictogram) quantities of DNA.Molecular Bioscience

Elliptical Thinking: Planetary Patterns of Thought in De Profundis

In an 1881 letter asking a friend to meet his mother, Oscar Wilde writes: ‘all brilliant people should cross each other’s cycles, like some of the nicest planets’. In comparing the people in his social circle to celestial bodies in orbit, Wilde sets forth an idea that will soon become literalized in images within and surrounding his works. An illustration in Salomé (1894) renders Wilde the actual ‘(wo)man in the moon’, through placing his distinguishing physiognomy – slightly drooping eyes and thick full lips – on a white circle [fig. 1], while many cartoons satirizing Wilde’s American lecture tour put his head at the centre of a plant that seems to be more sun than flower. An 1881 Punch cartoon by Edward Sambourne, ‘O.W.’, features Wilde’s head as the only visible centre of a sunflower, with crisp triangular petals extending outward so rigidly that they appear to emanate from his body [fig. 2]. Another cartoon appearing in Judge magazine, entitled ‘A Thing of Beauty Not a Joy Forever’, features a sunflower-adorned Wilde standing with his head and torso in the centre of an enormous shape of ambiguous identification [fig. 3]. A very large orange circle with small yellow triangles coming off it, the shape could either be an enormous sunflower or, given its absence of a stem and leaves, a sun. Be he the face of the sun or the man in the moon, Wilde is, in all three of these illustrations, combined with a celestial body

Letter from Amelia A. Hall, 1880-11-02, Wellesley, Ma., to Dear Mother

Wellesley, Mass Nov 2, 1880 My Dear Mother, In the few minutes left before chapel, I’m going to begin this letter to you and there is little doubt but that I’ll have time enough to finish it this evening, for I know all my lessons for tomorrow and after chapel I shall be left to my own devices, for Hat is going to a lecture by Dr. Duryea and no freshmen are admitted nor in fact is anybody but seniors, teachers, and teacher specials. Are you filled with excitement politically as to the result of the coming election? If you should make it through the usually sedate looking corridors of Wellesley at the present [page break] you might arrive at some faint idea at what an interest the girls are taking in politics. From the [?] of many doors to those opposite are suspended red white and blue shawls festooned in all manners of artistic arrays, - with pictures of Garfield or Hancock as the sympathies of the inmates[?] go. Many of the dorms themselves are covered with flags, effigies, portraits and various other decorations. Jennie Hays and Anna Nhuler room opposite us, and we thought we might as well be out of the world as out of the fashion, so we too have stretched across a wide red scarf festooned with a blue and white one and covered with all the red and blue ribbons in our joint possession. Our dorm is resplendent with hats [page break] red and white hoods looped up with blue ribbons and with a festoon of navy blue where on are basted letters spelling Garfield and Arthur, and so too is the dorm opposite and the same names gleam from our showpiece. Upstairs there is one door where a parasol arranged like a parachute is suspended across the corridor and from it hangs an effigy of Hancock with the inscription “Hancock gone up.” Then we have an elegant standard manufactured,-breathe it gently,-of a broom!!The brush is covered with Jennie’s red flannel petticoat and the stick is wound with red white and blue stockings belonging to both sides. This too has a Garfield placard. But the funniest is when a democrat and republican room together then the display is very funny. [page break] I’ve told you quite enough of this however, so let me change the subject. You probably know that during the past week the Women’s Temperance Union has been having it’s annual meeting in Boston. And last evening Miss Grace Greenwood and Mrs. Barnes were here, they spoke to us very interestingly and Miss Greenwood was so much pleasured with our political decorations that she asked Miss Howard to let us vote this morning at breakfast, so we did; and with this result, 317 for Garfield and 52 for Hancock. You ask about mathematics and music. The former I find about as usual, not very hard; but Miss Hayes-this is private-complimented me quite highly several times, so I feel quite pleased. The music is hard, but I think I make progress, anyway I try very hard and hope to be able to play you something pretty by the time I come home x mas which will be very soon now. Do all take very good care of yourselves, so many of the girls have been called home by sudden deaths-[?] girls from Canada who sit at our table have just within the last four days heard of the death of their father and the worst of it was the letter was miscarried and[?] delayed and they did not receive the letters till after his burial. They of course are not going home now. I feel so very sorry for them. The rest of us at the table sent them a beautiful bunch of hot house flowers yesterday.-as a token of our sympathies. I cannot write more tonight except to tell you that the present at least, I’ve entirely recovered from my rheumatism and if Hat were here she’d send her love as I do to all the home. Your Amelia- [Written in the top margin of page two] Amelia’s rheumatism has only interfered with her practice one day and she is much better now. I have just returned from the lecture on “Mental Science” which as usual was just splendid. Yours, H.H

The Effect of Dance and Exercise to Music on Mood in Those with Parkinson's Disease

The aim of this thesis was to investigate the effect of dance and exercise to music on mood in those with Parkinson’s disease (PD). A series of five studies were conducted in order to explore whether there are physical and psychological benefits of dance and exercise to music for those with PD. This programme of research collected data in a variety of ways, over a number of weeks (study one – 10 weeks), through survey data (study two) and in peoples own homes (study three, four and five). These studies have focused on the effect of these activities on mood and as the programme of research developed, the role of socialisation became a key factor. These studies have concluded that mood is significantly improved following dance and movement to music, but that this may be moderated by social interaction. Mood effects observed during a social dance class initially appeared to be comparable to 30 minutes of exercise to music at home. This suggests that music and movement without the social aspect of a class could also evoke an improvement in mood. After further investigation, however, it appeared that mood may have been affected by the presence of the researcher as a social factor. Overall, this programme of research has suggested that dance and music to movement is a beneficial form of activity but that the social aspect of this is imperative to have an effect on mood

Digital Dissections Using Voyant

This assignment sequence consists of two lab report writing assignments, an informal writing assignment on endings, an introduction to digital humanities handout, and a “How to Perform a digital dissection” handout, all of which prepare students to write a literary analysis essay about The Island of Doctor Moreau

Planet formation: The case for large efforts on the computational side

Modern astronomy has finally been able to observe protoplanetary disks in reasonable resolution and detail, unveiling the processes happening during planet formation. These observed processes are understood under the framework of disk-planet interaction, a process studied analytically and modeled numerically for over 40 years. Long a theoreticians' game, the wealth of observational data has been allowing for increasingly stringent tests of the theoretical models. Modeling efforts are crucial to support the interpretation of direct imaging analyses, not just for potential detections but also to put meaningful upper limits on mass accretion rates and other physical quantities in current and future large-scale surveys. This white paper addresses the questions of what efforts on the computational side are required in the next decade to advance our theoretical understanding, explain the observational data, and guide new observations. We identified the nature of accretion, ab initio planet formation, early evolution, and circumplanetary disks as major fields of interest in computational planet formation. We recommend that modelers relax the approximations of alpha-viscosity and isothermal equations of state, on the grounds that these models use flawed assumptions, even if they give good visual qualitative agreement with observations. We similarly recommend that population synthesis move away from 1D hydrodynamics. The computational resources to reach these goals should be developed during the next decade, through improvements in algorithms and the hardware for hybrid CPU/GPU clusters. Coupled with high angular resolution and great line sensitivity in ground based interferometers, ELTs and JWST, these advances in computational efforts should allow for large strides in the field in the next decade.Comment: White paper submitted to the Astro2020 decadal surve

Structural and magnetic investigations of chiral magnets

Investigations of the magnetic structures and phase diagrams of chiral magnetic materials has led to the discovery of topological magnetic phenomena such as skyrmions and the chiral soliton lattice, which are of interest for spintronics device applications. In this thesis, the structural and magnetic properties of several chiral magnetic materials are explored, focusing on the intercalated transition metal dichalcogenides and the frustrated antiferromagnetic Mn3XY (X =Rh,Ir, Y =Si,Ge) families of materials. Firstly, the magnetic structure of V1=3NbS2 is studied and found to display behaviour consistent with a canted antiferromagnet. Two propagation vectors are required to index all the magnetic Bragg peaks present in powder neutron di_raction data; the k0 = (0,0,0) propagation vector is associated with an in-plane A-type antiferromagnetic ordering, while the k1=3 = (0,0,1/3) magnetic propagation vector can be associated with an up-down-down con_guration of moments along the c axis. A ferromagnetic component too small to be resolved in these measurements is expected from magnetisation data. This thesis goes on to describe a detailed structural and magnetic investigation to compare single crystals of Mn1=3NbS2, Cr1=3NbS2, and Cr1=3TaS2. Lorentz transmission electron microscopy measurements show the presence of helimagnetic ordering in Cr1=3NbS2 below TC = 111 K, while there is no evidence that Mn1=3NbS2 exhibits helimagnetic ordering below TC = 45 K. An analogue is drawn between the magnetic phase diagrams of Cr1=3NbS2, Cr1=3TaS2, and Mn1=3NbS2, constructed from ac susceptibility measurements. Finally, this thesis describes an investigation into Mn3IrSi, Mn3RhGe, and Mn3RhSi. A single crystal of Mn3RhSi has been successfully grown and its magnetic properties investigated with dc susceptibility measurements to show a magnetic transition at 228 K. Powder neutron di_raction investigations into polycrystalline Mn3IrSi and Mn3RhGe reveal a three-dimensional frustrated antiferromagnetic ground state for both materials, while Mn3RhGe exhibits an incommensurate helical magnetic phase at 200 K

Women gaze behaviour in assessing female bodies: the effects of clothing, body size, own body composition and body satisfaction

Often with minimally clothed figures depicting extreme body sizes, previous studies have shown women tend to gaze at evolutionary determinants of attractiveness when viewing female bodies, possibly for self-evaluation purposes, and their gaze distribution is modulated by own body dissatisfaction level. To explore to what extent women’s body-viewing gaze behaviour is affected by clothing type, dress size, subjective measurements of regional body satisfaction and objective measurements of own body composition (e.g., chest size, body mass index, waist-to-hip ratio), in this self-paced body attractiveness and body size judgement experiment, we compared healthy, young women’s gaze distributions when viewing female bodies in tight and loose clothing of different dress sizes. In contrast to tight clothing, loose clothing biased gaze away from the waist-hip to the leg region, and subsequently led to enhanced body attractiveness ratings and body size underestimation for larger female bodies, indicating the important role of clothing in mediating women’s body perception. When viewing preferred female bodies, women’s higher satisfaction of a specific body region was associated with an increased gaze towards neighbouring body areas, implying satisfaction might reduce the need for comparison of confident body parts; furthermore undesirable body composition measurements were correlated with a gaze avoidance process if the construct was less changeable (i.e. chest size) but a gaze comparison process if the region was more changeable (i.e. body mass index, dress size). Clearly, own body satisfaction and body composition measurements had an evident impact on women’s body-viewing gaze allocation, possibly through different cognitive processes

Complex Reorganization and Predominant Non-Homologous Repair Following Chromosomal Breakage in Karyotypically Balanced Germline Rearrangements and Transgenic Integration

We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically-interpreted translocations and inversions. We confirm that the recently described phenomenon of “chromothripsis” (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline where it can resolve to a karyotypically balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign CNVs. We compared these results to experimentally-generated DNA breakage-repair by sequencing seven transgenic animals, and revealed extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion is the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations