Seven exercises planned to stimulate the flow of ideas in creative composition

Thesis (Ed.M.)--Boston Universit

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences

Background Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats). Results In this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure. Conclusions PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available

Chromosome Segregation Is Biased by Kinetochore Size

Chromosome missegregation during mitosis or meiosis is a hallmark of cancer and the main cause of prenatal death in humans. The gain or loss of specific chromosomes is thought to be random, with cell viability being essentially determined by selection. Several established pathways including centrosome amplification, sister-chromatid cohesion defects, or a compromised spindle assembly checkpoint can lead to chromosome missegregation. However, how specific intrinsic features of the kinetochore—the critical chromosomal interface with spindle microtubules—impact chromosome segregation remains poorly understood. Here we used the unique cytological attributes of female Indian muntjac, the mammal with the lowest known chromosome number (2n = 6), to characterize and track individual chromosomes with distinct kinetochore size throughout mitosis. We show that centromere and kinetochore functional layers scale proportionally with centromere size. Measurement of intra-kinetochore distances, serial-section electron microscopy, and RNAi against key kinetochore proteins confirmed a standard structural and functional organization of the Indian muntjac kinetochores and revealed that microtubule binding capacity scales with kinetochore size. Surprisingly, we found that chromosome segregation in this species is not random. Chromosomes with larger kinetochores bi-oriented more efficiently and showed a 2-fold bias to congress to the equator in a motor-independent manner. Despite robust correction mechanisms during unperturbed mitosis, chromosomes with larger kinetochores were also strongly biased to establish erroneous merotelic attachments and missegregate during anaphase. This bias was impervious to the experimental attenuation of polar ejection forces on chromosome arms by RNAi against the chromokinesin Kif4a. Thus, kinetochore size is an important determinant of chromosome segregation fidelity

A kinematically selected, metal-poor stellar halo in the outskirts of M31

We present evidence for a metal-poor, [Fe/H]$\sim-1.4$ $\sigma$=0.2 dex, stellar halo component detectable at radii from 10 kpc to 70 kpc, in our nearest giant spiral neighbor, the Andromeda galaxy. This metal-poor sample underlies the recently-discovered extended rotating component, and has no detected metallicity gradient. This discovery uses a large sample of 9861 radial velocities of Red Giant Branch (RGB) stars obtained with the Keck-II telescope and DEIMOS spectrograph, with 827 stars with robust radial velocity measurements isolated kinematically to lie in the halo component primarily by windowing out the extended rotating component which dominates the photometric profile of Andromeda out to $<$50 kpc (de-projected). The stars lie in 54 spectroscopic fields spread over an 8 square degree region, and are expected to fairly sample the halo to a radius of $\sim$70 kpc. The halo sample shows no significant evidence for rotation. Fitting a simple model in which the velocity dispersion of the component decreases with radius, we find a central velocity dispersion of 152\kms decreasing by -0.90\kms/\kpc. By fitting a cosmologically-motivated NFW halo model to the halo stars we constrain the virial mass of M31 to be greater than 9.0 \times 10^{11} \msun with 99% confidence. The properties of this halo component are very similar to that found in our Milky Way, revealing that these roughly equal mass galaxies may have led similar accretion and evolutionary paths in the early Universe.Comment: 13 pages, 12 figures, accepted in ApJ. substantially revised versio

Struktur Komunitas Makrozoobentos sebagai Bioindikator Kualitas Air di Sungai Way Awi, Bandarlampung

Makrozoobentos merupakan invertebrata yang masa hidupnya dihabiskan di dasar perairan atau di atas sedimen. Penelitian ini bertujuan untuk mengkaji struktur komunitas makrozoobentos sebagai bioindikator kualitas air di Sungai Way Awi, Bandarlampung. Penelitian dilakukan pada Oktober-Desember 2023. Pengambilan sampel makrozoobentos menggunakan Ekman grab di lima stasiun mewakili hulu, tengah, dan hilir sungai. Analisis dan identifikasi sampel dilakukan di Laboratorium Zoologi FMIPA Universitas Lampung dengan bantuan buku identifikasi Fresh-Water Biology. Hasil penelitian berhasil mengidentifikasi 8 genus makrozoobentos yang terdiri dari phylum Mollusca, Arthropoda, dan Annelida. Struktur komunitas menunjukkan kondisi indeks keanekaragaman yang rendah (H’ &lt; 1), indeks keseragaman sedang hingga tinggi (0,4 &lt; E &lt; 1), indeks dominansi sedang hingga tinggi (0,30 &lt; C &lt; 1), dan indeks kekayaan jenis rendah (Dmg &lt; 2,05). Analisis korelasi antara struktur komunitas dan pengukuran sifat fisika-kimia badan air menunjukkan adanya hubungan signifikan antara oksigen terlarut (DO) dengan indeks keseragaman dan indeks dominansi. Berdasarkan hasil tersebut dapat disimpulkan bahwa parameter fisika-kimia perairan memiliki peran dalam menentukan struktur komunitas makrozoobentos dan dapat dijadikan sebagai indikator dalam penilaian kualitas air

The Metal-Poor Halo of the Andromeda Spiral Galaxy (M31)

We present spectroscopic observations of red giant branch (RGB) stars over a large expanse in the halo of the Andromeda spiral galaxy (M31), acquired with the DEIMOS instrument on the Keck II 10-m telescope. Using a combination of five photometric/spectroscopic diagnostics -- (1) radial velocity, (2) intermediate-width DDO51 photometry, (3) Na I equivalent width (surface gravity sensitive), (4) position in the color-magnitude diagram, and (5) comparison between photometric and spectroscopic [Fe/H] estimates -- we isolate over 250 bona fide M31 bulge and halo RGB stars located in twelve fields ranging from R = 12-165kpc from the center of M31 (47 of these stars are halo members with R > 60 kpc). We derive the photometric and spectroscopic metallicity distribution function of M31 RGB stars in each of these fields. The mean of the resulting M31 spheroid (bulge and halo) metallicity distribution is found to be systematically more metal-poor with increasing radius, shifting from = -0.47+/-0.03 (sigma = 0.39) at R = -0.94+/-0.06 (sigma = 0.60) at R ~ 30 kpc to = -1.26+/-0.10 (sigma = 0.72) at R > 60 kpc, assuming [alpha/Fe] = 0.0. These results indicate the presence of a metal-poor RGB population at large radial distances out to at least R = 160 kpc, thereby supporting our recent discovery of a stellar halo in M31: its halo and bulge (defined as the structural components with R^{-2} power law and de Vaucouleurs R^{1/4} law surface brightness profiles, respectively) are shown to have distinct metallicity distributions. If we assume an alpha-enhancement of [alpha/Fe] = +0.3 for M31's halo, we derive = -1.5+/-0.1 (sigma = 0.7). Therefore, the mean metallicity and metallicity spread of this newly found remote M31 RGB population are similar to those of the Milky Way halo.Comment: Accepted for publication in ApJ on May 4th, 2006 (submitted on Jan 30, 2006). 16 pages, 13 figures, 3 table

Tracing Galaxy Formation with Stellar Halos II: Relating Substructure in Phase- and Abundance-Space to Accretion Histories

This paper explores the mapping between the observable properties of a stellar halo in phase- and abundance-space and the parent galaxy's accretion history in terms of the characteristic epoch of accretion and mass and orbits of progenitor objects. The study utilizes a suite of eleven stellar halo models constructed within the context of a standard LCDM cosmology. The results demonstrate that coordinate-space studies are sensitive to the recent (0-8 Gyears ago) merger histories of galaxies (this timescale corresponds to the last few to tens of percent of mass accretion for a Milky-Way-type galaxy). Specifically, the {\it frequency, sky coverage} and {\it fraction of stars} in substructures in the stellar halo as a function of surface brightness are indicators of the importance of recent merging and of the luminosity function of infalling dwarfs. The {\it morphology} of features serves as a guide to the orbital distribution of those dwarfs. Constraints on the earlier merger history (> 8 Gyears ago) can be gleaned from the abundance patterns in halo stars: within our models, dramatic differences in the dominant epoch of accretion or luminosity function of progenitor objects leave clear signatures in the [alpha/Fe] and [Fe/H] distributions of the stellar halo - halos dominated by very early accretion have higher average [alpha/Fe], while those dominated by high luminosity satellites have higher [Fe/H]. This intuition can be applied to reconstruct much about the merger histories of nearby galaxies from current and future data sets.Comment: 21 pages, 20 figures. To appear in the Astrophysical Journa