A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BACKGROUND: Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6x coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process. RESULTS: An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6x bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map. CONCLUSION: Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

An Isopach Map and Discussion of the Marine Jurassic of Western United Sates and Canada

Recent demands for petroleum to carry on the war effort have resulted in widespread prospecting in the northern Great Plains. Nearly all oil wells now drilled are of a depth to penetrate the marine Jurassic formations. It is known that these strata differ in thickness from place to place, but information of distribution, thickness, and lithology has not yet been compiled.

An Isopach Map and a Discussion of the Permian in Wyoming and Adjacent Areas

The accelerated post-war demand for petroleum products with resultant high prices and dwindling reserves has spurred producers to an extensive search for new fields and for ad­ditional production in known fields. Exploration and discov­ery is dependent on the collection and correlation of vast amounts of data both in the field and that found in liter­ature.

Razor Thin Win: The 1972 Constitution Ballot, Campaign, Ratification & the Courts -- Mae Nan (Robinson) Ellingson & Mick McKeon “In the Crucible of Change”

Beyond the challenge of crafting a new state Constitution that empowered the people and modernized and opened up state and local government in Montana, the Constitutional Convention delegates, as they signed the final document, looked forward to the arduous task of getting it ratified by the electorate in a short ten week period between the end of the convention on March 24 and the ratification election of June 6, 1972. While all 100 delegates signed the draft Constitution, not all supported its adoption. But the planning about how to get it adopted went back to the actions of the Convention itself, which carefully crafted a ballot that kept “hot political issues” from potentially killing the entire document at the polls. As a result, three side issues were presented to the electorate on the ballot. People could vote for or against those side issues and still vote to ratify the entire document. Thus, the questions of legalizing gambling, having a unicameral legislature and retaining the death penalty were placed separately on the ballot (gambling passed, as did the retention of the death penalty, but the concept of a one-house legislature was defeated). Once the ballot structure was set, delegates who supported the new Constitution organized a grassroots, locally focused effort to secure ratification – thought hampered by a MT Supreme Court decision on April 28 that they could not expend $45,000 in public monies that they had set aside for voter education. They cobbled together about $10,000 of private money and did battle with the established political forces, led by the MT Farm Bureau, MT Stockgrowers’ Assn. and MT Contractors Assn., on the question of passage. Narrow passage of the main document led to an issue over certification and a Montana Supreme Court case challenging the ratification vote. After a 3-2 State Supreme Court victory, supporters of the Constitution then had to defend the election results again before the federal courts, also a successful effort. Montana finally had a new progressive State Constitution that empowered the people, but the path to it was not clear and simple and the win was razor thin. The story of that razor thin win is discussed in this chapter by the two youngest delegates to the 1972 Constitutional Convention, Mae Nan Ellingson of Missoula and Mick McKeon, then of Anaconda. Both recognized “Super Lawyers in their later professional practices were also significant players in the Constitutional Convention itself and actively participated in its campaign for ratification. As such, their recollections of the effort provide an insider’s perspective of the struggle to change Montana for the better through the creation and adoption of a new progressive state Constitution “In the Crucible of Change.” Mae Nan (Robinson) Ellingson was born Mae Nan Windham in Mineral Wells, TX and graduated from Mineral Wells High School in 1965 and Weatherford College in Weatherford, TX in 1967. Mae Nan was the youngest delegate at the 1972 Convention from Missoula. She moved to Missoula in 1967 and received her BA in Political Science with Honors from the University of MT in 1970. She was a young widow known by her late husband’s surname of Robinson while attending UM graduate school under the tutelage of noted Professor Ellis Waldron when he persuaded her to run for the Constitutional Convention. Coming in a surprising second in the delegate competition in Missoula County she was named one of the Convention’s “Ten Outstanding Constitutional Convention Delegates,” an impressive feat at such a young age. She was 24 at the time, the youngest person to serve at the ConCon, and one of 19 women out of 100 delegates. In the decade before the Convention, there were never more than three women Legislators in any session, usually one or two. She was a member of the American Association of University Women, a Pi Sigma Alpha political science honorary, and a Phi Alpha Theta historical honorary. At the Convention, she led proposals for the state's bill of rights, particularly related to equal rights for women. For years, Ellingson kept a copy of the preamble to the Constitution hanging in her office; while all the delegates had a chance to vote on the wording, she and delegate Bob Campbell are credited with the language in the preamble. During the convention, she had an opportunity that opened the door to her later career as an attorney. A convention delegate suggested to her that she should go to law school. Several offered to help, but at the time she couldn't go to school. Her mom had died in Texas, and she ended up with a younger brother and sister to raise in Missoula. She got a job teaching, but about a year later, intrigued with the idea of pursuing the law as a career, she called the man back to ask about the offer. Eventually another delegate, Dave Drum of Billings, sponsored her tuition at the UM School of Law. After receiving her JD with Honors (including the Law Review and Moot Court) from the UM Law School Ellingson worked for the Missoula city attorney's office for six years (1977-83), and she took on landmark projects. During her tenure, Missoula became the first city to issue open space bonds, a project that introduced her to Dorsey & Whitney. The city secured its first easement on Mount Sentinel, and it created the trail along the riverfront with a mix of playing fields and natural vegetation. She also helped develop a sign ordinance for the city of Missoula. She ended up working as bond counsel for Dorsey & Whitney, and she opened up the firm's full-fledged Missoula office after commuting a couple of years to its Great Falls office. She was a partner at Dorsey Whitney, working there from 1983 until her retirement in 2012. The area of law she practiced there is a narrow specialty - it requires knowledge of constitutional law, state and local government law, and a slice of federal tax law - but for Ellingson it meant working on great public projects – schools, sewer systems, libraries, swimming pools, ire trucks. At the state level, she helped form the Montana Municipal Insurance Authority, a pooled insurance group for cities. She's shaped MT’s tax increment law, and she was a fixture in the MT Legislature when they were debating equal rights. As a bond lawyer, though, Ellingson considers her most important work for the state to be setting up the Intercap Program that allowed local governments to borrow money from the state at a low interest rate. She has been a frequent speaker at the League of Cities and Towns, the Montana Association of Counties, and the Rural Water Users Association workshops on topics related to municipal finance, as well as workshops sponsored by the DNRC, the Water and Sewer Agencies Coordination Team, and the Montana State University Local Government Center. In 2002, she received an outstanding service award from the Montana Rural Water Users Association. In addition to being considered an expert on Montana state and constitutional law, local government law and local government finance, she is a frequent teacher at the National Association of Bond Lawyers (NABL) Fundamentals of Municipal Bond Law Seminar and the NABL Bond Attorney’s Workshop. For over 30 years Mae Nan has participated in the drafting of legislation in Montana for state and local finance matters. She has served on the Board of Directors of NABL, as Chairman of its Education Committee, was elected as an initial fellow in 1995 to the American College of Bond Counsel, and was recognized as a Super Lawyer in the Rocky Mountain West. Mae Nan was admitted to practice before the MT and US Supreme Courts, was named one of “America’s Leading Business Lawyers” by Chambers USA (Rank 1), a Mountain States Super Lawyer in 2007 and is listed in Best Lawyers in America; she is a member and former Board Member of NABL, a Fellow of the American College of Bond Counsel and a member of the Board of Visitors of the UM Law School. Mae Nan is also a philanthropist who serves on boards and applies her intelligence to many organizations, such as the Missoula Art Museum. [Much of this biography was drawn from a retirement story in the Missoulian and the Dorsey Whitney web site.] Mick McKeon, born in Anaconda in 1946, is a 4th generation Montanan whose family roots in this state go back to the 1870’s. In 1968 he graduated from Notre Dame with a BA in Communications and received a Juris Doctorate degree from the University of Montana Law School in 1971. Right after graduating from law school, Mick was persuaded by his father, longtime State Senator Luke McKeon, and his uncle, Phillips County Attorney Willis McKeon, to run for delegate to Montana’s Constitutional Convention and was elected to represent Deer Lodge, Philipsburg, Powell, and part of Missoula Counties. Along with a coalition of delegates from Butte and Anaconda, he fought through the new Constitution to eliminate the legal strangle hold, often called “the copper collar,” that corporate interests -- the Anaconda Company and its business & political allies -- had over state government for nearly 100 years. The New York Times called Montana’s Constitutional Convention a “prairie revolution.” After helping secure the ratification of the new Constitution, Mick began his practice of law in Anaconda where he engaged in general practice for nearly 20 years. Moving to Butte in 1991, Mick focused has practice in personal injury law, representing victims of negligence and corporate wrongdoing in both Montana district courts and federal court. As such, he participated in some of the largest cases in the history of the state. In 1992 he and his then law partner Rick Anderson obtained a federal court verdict of $11.5 million -- the largest verdict in MT for many years. Mick’s efforts on behalf of injured victims have been recognized by many legal organizations and societies. Recently, Mick was invited to become a member of the International Academy of Trial Lawyers - 600 of the top lawyers in the world. Rated as an American Super Lawyer, he has continuously been named one of the Best Lawyers in America, and an International Assn. of Trial Lawyers top 100 Trial Lawyer. In 2005, he was placed as one of Montana’s top 4 Plaintiff’s lawyers by Law Dragon. Mick is certified as a civil trial specialist by the National Board of Trial Advocacy and has the highest rating possible from Martindale-Hubble. Mick was awarded the Montana Trial Lawyers Public Service Award and provided pro bono assistance to needy clients for his entire career. Mick’s law practice, which he now shares with his son Michael, is limited to representing individuals who have been injured in accidents, concentrating on cases against insurance companies, corporations, medical providers and hospitals. Mick resides in Butte with his wife Carol, a Butte native. Mick, Carol, Michael and another son, Matthew, who graduated from Dartmouth College and was recently admitted to the Montana bar, enjoy as much of their time together in Butte and at their place on Flathead Lake.

An Isopach Map and a Discussion of the Cambrian Strata in the Central Cordilleran Area

In the past few years intensive studies have been going on concerning Cambrian formations as a locale for orebodies. Many of the dolomites and limestones of southwestern Montana are susceptible to replacement by mineralizing solutions, especially when overlain by a rather impervious layer of shale, as is the Pilgrim limestone of Upper Cambrian time.

Human intervertebral disc stiffness correlates better with the Otsu threshold computed from axial T2 map of its posterior annulus fibrosus than with clinical classifications

Degeneration of the intervertebral disc, sometimes associated with low back pain and abnormal spinal motions, represents a major health issue with high costs. A non-invasive degeneration assessment via qualitative or quantitative MRI (magnetic resonance imaging) is possible, yet, no relation between mechanical properties and T2 maps of the intervertebral disc (IVD) has been considered, albeit T2 relaxation time values quantify the degree of degeneration. Therefore, MRI scans and mechanical tests were performed on 14 human lumbar intervertebral segments freed from posterior elements and all soft tissues excluding the IVD. Degeneration was evaluated in each specimen using morphological criteria, qualitative T2 weighted images and quantitative axial T2 map data and stiffness was calculated from the load-deflection curves of in vitro compression, torsion, lateral bending and flexion/extension tests. In addition to mean T2, the OTSU threshold of T2 (TOTSU), a robust and automatic histogram-based method that computes the optimal threshold maximizing the distinction of two classes of values, was calculated for anterior, posterior, left and right regions of each annulus fibrosus (AF). While mean T2 and degeneration schemes were not related to the IVDs' mechanical properties, TOTSU computed in the posterior AF correlated significantly with those classifications as well as with all stiffness values. TOTSU should therefore be included in future degeneration grading schemes.

The physical map of {\it Escherichia coli\/} K-12 strain MG1655: Construction, comparison with other strains and implications for mechanisms controlling oligonucleotide frequency

Complete NotI, SfiI, XbaI and BlnI cleavage maps of Escherichia coli K-12 strain MG1655 were constructed. Techniques used included: CHEF pulsed field gel electrophoresis; transposon mutagenesis; fragment hybridization to the ordered $\lambda$ library of Kohara et al.; fragment and cosmid hybridization to Southern blots; correlation of fragments and cleavage sites with EcoMap, a sequence-modified version of the genomic restriction map of Kohara et al.; and correlation of cleavage sites with DNA sequence databases. In all, 105 restriction sites were mapped and correlated with the EcoMap coordinate system.^ NotI, SfiI, XbaI and BlnI restriction patterns of five commonly used E. coli K-12 strains were compared to those of MG1655. The variability between strains, some of which are separated by numerous steps of mutagenic treatment, is readily detectable by pulsed-field gel electrophoresis. A model is presented to account for the difference between the strains on the basis of simple insertions, deletions, and in one case an inversion. Insertions and deletions ranged in size from 1 kb to 86 kb. Several of the larger features have previously been characterized and some of the smaller rearrangements can potentially account for previously reported genetic features of these strains.^ Some aspects of the frequency and distribution of NotI, SfiI, XbaI and BlnI cleavage sites were analyzed using a method based on Markov chain theory. Overlaps of Dam and Dcm methylase sites with XbaI and SfiI cleavage sites were examined. The one XbaI-Dam overlap in the database is in accord with the expected frequency of this overlap. The occurrence of certain types of SfiI-Dcm overlaps are overrepresented. Of the four subtypes of SfiI-Dcm overlap, only one has a partial inhibitory effect on the activity of SfiI. Recognition sites for all four enzymes are rarer than expected based on oligonucleotide frequency data, with this effect being much stronger for XbaI and BlnI than for NotI and SfiI. The latter two enzyme sites are rare mainly due to apparent negative selection against GGCC (both) and CGGCCG (NotI). The former two enzyme sites are rare mainly due to effects of the VSP repair system on certain di-tri- and tetranucleotides, most notably CTAG. Models are proposed to explain several of the anomalies of oligonucleotide distribution in E. coli, and the biological significance of the systems that produce these anomalies is discussed. ^

Psychomotor symptoms of schizophrenia map on the cerebral motor circuit

Schizophrenia is a devastating disorder thought to result mainly from cerebral pathology. Neuroimaging studies have provided a wealth of findings of brain dysfunction in schizophrenia. However, we are still far from understanding how particular symptoms can result from aberrant brain function. In this context, the high prevalence of motor symptoms in schizophrenia such as catatonia, neurological soft signs, parkinsonism, and abnormal involuntary movements is of particular interest. Here, the neuroimaging correlates of these motor symptoms are reviewed. For all investigated motor symptoms, neural correlates were found within the cerebral motor system. However, only a limited set of results exists for hypokinesia and neurological soft signs, while catatonia, abnormal involuntary movements and parkinsonian signs still remain understudied with neuroimaging methods. Soft signs have been associated with altered brain structure and function in cortical premotor and motor areas as well as cerebellum and thalamus. Hypokinesia is suggested to result from insufficient interaction of thalamocortical loops within the motor system. Future studies are needed to address the neural correlates of motor abnormalities in prodromal states, changes during the course of the illness, and the specific pathophysiology of catatonia, dyskinesia and parkinsonism in schizophrenia.

The identification and characterization of the Staphylococcus aureus microbial immunomodulatory molecules (MIMS) Map and Efb

Staphylococcus aureus is an opportunistic pathogen that is a major health threat in the clinical and community settings. An interesting hallmark of patients infected with S. aureus is that they do not usually develop a protective immune response and are susceptible to reinfection, in part because of the ability of S. aureus to modulate host immunity. The ability to evade host immune responses is a key contributor to the infection process and is critical in S. aureus survival and pathogenesis. This study investigates the immunomodulatory effects of two secreted proteins produced by S. aureus, the MHC class II analog protein (Map) and the extracellular fibrinogen-binding protein (Efb). Map has been demonstrated to modulate host immunity by interfering with T cell function. Map has been shown to significantly reduce T cell proliferative responses and significantly reduce delayed-type hypersensitivity responses to challenge antigen. In addition, the effects of Map on the infection process were tested in a mouse model of infection. Mice infected with Map− S. aureus (Map deficient strain) presented with significantly reduced levels of arthritis, osteomyelitis and abscess formation compared to mice infected with the wild-type Map+S. aureus strain suggesting that Map−S. aureus is much less virulent than Map+S. aureus. Furthermore, Map−S. aureus-infected nude mice developed arthritis and osteomyelitis to a severity similar to Map +S. aureus-infected controls, suggesting that T cells can affect disease outcome following S. aureus infection and Map may attenuate cellular immunity against S. aureus. The extracellular fibrinogen-binding protein (Efb) was identified when cultured S. aureus supernatants were probed with the complement component C3. The binding of C3 to Efb resulted in studies investigating the effects of Efb on complement activation. We have demonstrated that Efb can inhibit both the classical and alternative complement pathways. Moreover, we have shown that Efb can inhibit complement mediated opsonophagocytosis. Further studies have characterized the Efb-C3 binding interaction and localized the C3-binding domain to the C-terminal region of Efb. In addition, we demonstrate that Efb binds specifically to a region within the C3d fragment of C3. This study demonstrates that Map and Efb can interfere with both the acquired and innate host immune pathways and that these proteins contribute to the success of S. aureus in evading host immunity and in establishing disease. ^