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X-WR-CALNAME:Quantitative Biology Colloquium
X-WR-CALDESC:Quantitative Biology Colloquium Calendar, University of Arizon
 a Program in Applied Mathematics
X-WR-TIMEZONE:US/Arizona
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TZID:US/Arizona
BEGIN:STANDARD
DTSTART:19700101T000000
TZOFFSETFROM:-0700
TZOFFSETTO:-0700
TZNAME:MST
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BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:We are developing methods for defining transcriptional regulato
 ry networks underlying fundamental processes during embryonic development.
  Our general approach is to create a preliminary structure network (PSN) u
 sing a variety of biological information stores\, to iteratively sample th
 is and modified networks across parameter space\, and then to test success
 ful networks in vivo. A primary limitation for generation and modification
  of the PSN is the relative lack of interaction data in most model organis
 ms\, including chicken. To overcome this problem\, we have created integra
 ted interolog (interaction homolog) networks for all organisms represented
  in NCBI’s HomoloGene database using all available interaction data. 
 This has greatly increased the amount of interaction data available for th
 e twenty organisms currently in HomoloGene. We have also developed new alg
 orithms for more rapidly sampling networks in topology space and for measu
 ring their robustness with respect to changes in reaction rates. To measur
 e robustness efficiently\, we use approximations to the ODE systems that a
 re valid in a neighborhood\, and use the fact that re-optimizing is much l
 ess expensive than optimizing from scratch. Our methods are related to Mar
 kov Chain Monte Carlo sampling and Trust Regions. Preliminary results indi
 cate an improvement of an order of magnitude in terms of computing time\, 
 with only a marginal increase in variance.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080422T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Parker Antin\, Departments of Cell Biology and Anatomy and Molecula
 r and Cellular Biology\, and Leo Lopes\, Department of Systems and Industr
 ial Engineering: Network Modeling of Gene Regulatory Pathways in Vertebrat
 e Development
UID:20080423T203047CEST-faJJULeUoI@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:Adiponectin is a signalling hormone which stimulates the body's
  response to insulin and is of interest as a possible therapeutic for diab
 etes. Detailed knowledge of adiponectin's three-dimensional structure is p
 rerequisite to a mechanistic understanding of its physiological role. Howe
 ver\, its biochemical properties preclude the use of conventional experime
 ntal structure-determination methods. In this talk we will show how to dev
 elop new methods\, based on the differential geometry of curves\, to model
  the structure and mechanics of proteins. These methods are particularly w
 ell-suited to explore the properties of helical assembly. Starting with si
 mple helical structure (coils) we will show how we can construct higher-or
 der assemblies such as the ubiquitous coiled-coils\, a protein motif found
  in many fibrous proteins. The mechanical properties of such assemblies ca
 n be determined by developing a multiscale theory. The next higher-order a
 ssembly is the coiled-coiled-coil\, which we believe is applicable to adip
 onectin\, since it exists in serum in three distinct oligomeric states wit
 h 3\, 6\, and 18 protein subunits.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080415T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Andrew Hausrath\, Department of Biochemistry and Molecular Biophysi
 cs\, and Alain Goriely\, Department of Mathematics: Coils\, Coiled-coils\,
  and Coiled-coiled-coils: Unraveling the Hierarchical Structure of Adipone
 ctin
UID:20080423T203047CEST-S92aVHexVW@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:In 1973 Karl von Frisch was awarded the Nobel Prize in Physiolo
 gy for his work decoding the 'language' of bees.  The language of bees\, a
 lso known as the 'waggle dance\,' is used by foraging honeybees to indicat
 e the distance and direction of a food source to other bees in the hive. S
 ince then we have learned from numerous behavioral studies that a honeybee
 's judgment of distance is based on a visual estimate of speed. This estim
 ate is relatively independent of spatial frequency\, contrast\, and direct
 ion of motion and can even be made with only monocular input.\n\nDespite o
 ur thorough understanding of the many behaviors that rely on visual speed 
 estimation\, we still lack a solid understanding of the underlying neural 
 processes responsible for the estimate. My research has focused on evaluat
 ing various models of visual speed estimation based on their effectiveness
  for replicating\, in simulation\, the behaviors observed in honeybees. I 
 then use the results from the simulations to generate hypotheses and exper
 iments to further refine the models. In addition\, I have recently begun m
 y own behavioral work to gather more detailed information on the propertie
 s of the honeybee speedometer.\n
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080408T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Jonathan Dyhr: Visual Speedometers in the Honeybee Brain
UID:20080423T203047CEST-536o2Kmd6h@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:Using the compiled human genome sequence\, we systematically ca
 talogued all tandem repeats with periods between 20 and 2\,000 bp and defi
 ned two subsets whose pattern sequences were found at either single (slTRs
 ) or multiple loci(mlTRs).  Parameters compiled for these subsets are cons
 istent with a two step model for their evolution beginning with an initial
  duplication event insensitive to the unique or repetitive nature of the n
 ascent sequence. Subsequent amplification steps via gene conversion are in
 frequent and can create new alleles varying in both repeat number and inte
 rnal sequence.  Tandem repeats are non-randomly distributed in the genome\
 ; both subsets are found at higher frequency at many but not all chromosom
 e ends and internal clusters of mlTRs are also seen. Despite the integral 
 role of recombination in the biology of tandem repeats\, recombination hot
 spots co-localized only with shorter microsatellites and not the longer re
 peats examined here. An increased frequency of slTRs was observed near imp
 rinted genes\, consistent with a functional role\, while both slTRs and ml
 TRs were found more frequently near genes implicated in triplet expansion 
 diseases\, suggesting a general instability of these regions. Using our co
 llated parameters\, we identified 2\,230 slTRs as candidates for highly in
 formative molecular markers.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080311T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Vicki Chandler: Genome-Wide Analyses of Tandem Repeats in Humans
UID:20080423T203047CEST-c3vUReB5DD@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:The reality of global warming\, reflected in a broad spectrum o
 f climate system change\, is now unequivocal. Moreover\, human complicity 
 in global warming has also been established beyond a reasonable doubt. Wit
 h these and other advances embodied in the Intergovernmental Panel on Clim
 ate Change Fourth Assessment Report (IPCC AR4) has come a shift in scienti
 fic focus toward efforts designed to improve our understanding of what wil
 l happen in the future\, and to what can be done to deal with the reality 
 of global to regional climate change. Major efforts are now needed to deve
 lop strategies for adapting to climate change that is already in the pipel
 ine\, and also to identify climate changes that may be deemed unacceptable
 \, and thus worthy drivers of mitigation strategies designed to reduce the
  rate of atmospheric greenhouse gas increases to 'safe' levels.\n\nThere m
 ay be many aspects of future global climate change that will ultimately be
  deemed undesirable and worthy of mitigation efforts\, but two major issue
 s are already coming into focus. The first is global sea level rise couple
 d with increasing tropical storm intensities. There is no doubt that globa
 l sea level is rising\, and little doubt that the rates of sea level rise 
 are likely to increase. In contrast to what some biased media and individu
 als are saying\, the IPCC AR4 did not lower estimates of future sea level 
 rise. Indeed\, the most recent estimates suggest that 1m or more of sea le
 vel rise could occur by 2100\, as well as a commitment to a much larger se
 a level rise over subsequent centuries. The wildcard will be the future be
 havior of the large polar ice sheets\, and there is growing evidence that 
 the ice sheets are more vulnerable to global warming than widely thought.\
 n\nAlthough coastal areas could thus be big losers in the face of continue
 d climate change\, recent climate change coupled with climate change proje
 ctions indicate that the American West--including the alpine West--could b
 e a more near-term casualty. Surface air temperatures are already rising f
 aster than elsewhere in the coterminous United States\, and will likely co
 ntinue to rise steadily. These temperature increases are already causing s
 now to fall increasingly as rain\, and also to melt earlier in the year. T
 hus\, even in the absence of a precipitation decrease\, there will be less
  snow-related run-off and related surface water flow. This trend is also b
 eing exacerbated in some parts of the West by human-caused increases in at
 mospheric dust loading. Unfortunately\, nearly all state-of-the-art climat
 e models being forced with increasing greenhouse gases (and other human-ca
 used pollution) are also simulating a steady decline in average wintertime
  precipitation in the Southwest. More troubling is the fact that these sim
 ulated changes are also in accord with what has been happening in the real
  world-- there is a growing scientific consensus that winters will become 
 much hotter and significantly drier due to the greenhouse-gas climate forc
 ing. On top of these trends in average condition is the likelihood that mu
 lti-year\, even multi-decade\, drought will also become more common. Thus\
 , the recent western drought--already the worst of the instrumental era--c
 ould be a harbinger of greater aridity to come\, and also a significant th
 reat to the West as we know it. Fortunately\, there are solutions if we ch
 oose to act aggressively.\n
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080304T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Jonathan Overpeck: Climate Change\, Sea Level\, and Western Drought
 : Dangerous Anthropogenic Interference?
UID:20080423T203047CEST-LTlJU99cnO@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:Molecular marker data is exceptional at determining whether a b
 iological sample (such as blood or an offspring!) came from a specified in
 dividual. Genealogists have become very interested in using molecular data
  to assess slightly more distant relationships\, those within 3-20 generat
 ions. I'll review why this is done using collections of completely linked 
 markers (such as the Y chromosome) and discuss various statistical models 
 for estimating the time to the most recent common ancestor given two such 
 sequences. We start with a simple maximum likelihood approach\, discover i
 ts flaws\, and then develop a fully Bayesian estimator that addresses thes
 e concerns.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080226T041500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Bruce Walsh: Who's Your Great-great-great Granddaddy?  Estimation o
 f Time to Most Recent Common Ancestor Given Molecular Genealogical Data
UID:20080423T203047CEST-i31gs1CVVU@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:We have investigated the effect of DNA tension upon the associa
 tion and dissociation of the T7 RNA polymerase/promoter DNA interaction. U
 sing two optically trapped beads\, we suspended a single DNA molecule cont
 aining the T7-phi13 promoter above a 3rd surface-immobilized bead that bea
 rs active molecules of T7 RNAP. The DNA was brought into contact with the 
 surface bead\, while applying a 50 Hz triangle oscillation to the bead ups
 tream of the promoter. Binding of T7 RNAP at the promoter was detected as 
 the decoupling of motion of the two optically trapped beads: oscillations 
 of the downstream bead are reduced or cease altogether upon binding. The D
 NA tension upon binding is directly proportional to the displacement of th
 e downstream bead from the center of the optical trap. By altering both th
 e mean tension in the DNA--changing trap stiffness or the mean bead-to-bea
 d distance--we have been able to observe promoter binding across the range
  of force 1-12 pN. From these data we find clear evidence that the mean li
 fetime of the promoter/T7 RNAP complex decreases with increasing tension a
 s indicated by an increasing dissociation rate constant\, koff\, from 3.5 
 s-1 at 1.5 pN up to 73 s-1 at >8 pN. From these observations\, we propose 
 that tension within a DNA molecule is able to regulate gene expression\, a
 t least in the case of the bacteriophage T7 enzyme. Based on the recent st
 ructural data of the T7 RNAP initiation complex we speculate on the mechan
 ism by which force may affect the dissociation kinetics.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080219T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Gary Skinner: Mechanical Tension within DNA Controls Gene Transcrip
 tion Initiation
UID:20080423T203047CEST-4LVOhs73XD@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:Magnetic resonance imaging (MRI) is a common and useful tool in
  medicine and biology. Typically\, when MRI images are used by a radiologi
 st to make a clinical diagnosis\, the analysis of the images is carried ou
 t qualitatively and relies heavily on the experience of the radiologist. A
 lthough quantitative information is available in MRI\, it is typically not
  obtained because of the increased data acquisition time required and the 
 ability of radiologists to make decisions without it. However\, in some ci
 rcumstances\, quantitative information can be very valuable in the diagnos
 is and evaluation of disease and in critical evaluation of therapy. A desc
 ription of quantitative parameters available from MRI experiments will be 
 presented\, and research projects in which they are being used will be dis
 cussed.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080212T161500
DURATION:PT1H
LOCATION:MRB 102
SUMMARY:Ted Trouard: Noninvasive Measurement of Tissue Properties with MRI
UID:20080423T203047CEST-Ub2zp8br3k@appliedmath.arizona.edu
END:VEVENT
BEGIN:VEVENT
CATEGORIES:Quantitative Biology
DESCRIPTION:In survival analysis\, censored observations can be regarded as
  missing event time data. We develop a direct approach\, multiple imputati
 on\, which shares common ideas with the redistribute to the right algorith
 m to recover information for censored observations. This approach can hand
 le both interval-censored and right-censored data. In one sample situation
 \, we show that with a large number of imputes the imputation method will 
 reproduce the Kaplan-Meier estimates. In interval-censored data situations
 \, we propose a nonparametric multiple imputation scheme\, NPMLE imputatio
 n. The imputation methods convert interval-censored data problems to compl
 eted data problems\, which enables estimates of measures of uncertainty to
  be more easily obtained. In a situation with auxiliary variables\, we inc
 orporate auxiliary variables into imputation through two working Cox propo
 rtional hazards models and show that the imputation method can reduce bias
  due to dependent censoring and improve the efficiency. These findings of 
 improved efficiency and reduced bias can be seen in both interval-censored
  and right-censored data. The methods are applied to AIDS data sets.
DTSTAMP:20080423T183047Z
DTSTART;TZID=US/Arizona:20080205T161500
DURATION:PT1H
LOCATION:Keating 103
SUMMARY:Chiu-Hsieh (Paul) Hsu: Survival Analysis via Multiple Imputation
UID:20080423T203047CEST-oalxJZuz4L@appliedmath.arizona.edu
END:VEVENT
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