Conservation genomics of natural and managed populations: building a conceptual and practical framework

The boom of massive parallel sequencing (MPS) technology and its applications in conservation of natural and managed populations brings new opportunities and challenges to meet the scientific questions that can be addressed. Genomic conservation offers a wide range of approaches and analytical techniques, with their respective strengths and weaknesses that rely on several implicit assumptions. However, finding the most suitable approaches and analysis regarding our scientific question are often difficult and time‐consuming. To address this gap, a recent workshop entitled ‘ConGen 2015’ was held at Montana University in order to bring together the knowledge accumulated in this field and to provide training in conceptual and practical aspects of data analysis applied to the field of conservation and evolutionary genomics. Here, we summarize the expertise yield by each instructor that has led us to consider the importance of keeping in mind the scientific question from sampling to management practices along with the selection of appropriate genomics tools and bioinformatics challenges.     

Mouse melanoma growth stimulatory activity gene (Mgsa) is polymorphic and syntenic with the W, patch, rumpwhite, and recessive spotting loci on chromosome 5

Melanoma growth stimulatory activity (Mgsa) is a polypeptide growth factor originally detected in culture medium of the human malignant melanoma cell line Hs294T and may have an autocrine role in neoplastic growth. Mgsa is a member of the small inducible gene (SIG) family and shares homology with beta-thromboglobulin and platelet factor 4. Mgsa was localized to chromosome 5 using a cDNA probe for mouse Mgsa and somatic cell hybrids and is thus syntenic with Kit (W), Ph, Rw, and rs loci. The results eliminate Mgsa as the product of the Steel locus on chromosome 10, but raise the possibility that Mgsa might be synonymous with a chromosome 5 locus affecting skin pigmentation.     

The DNF15S2 locus at 3p21 is transcribed in normal lung and small cell lung cancer

Small cell lung cancer (SCLC) has been associated with a deletion of the short arm of chromosome 3. One SCLC cell line, H748, has an interstitial deletion of chromosome 3p and shows allele loss for the DNF15S2 locus detected by the probe lambda H3. Conservation of DNF15S2 sequences in mouse indicated that this human genomic fragment may contain coding sequences. Screening of a normal lung cDNA library with chromosome 3-specific fragments of the lambda H3 probe resulted in the isolation of 18 positive clones. The cDNA clones detect an additional DNA polymorphism that is in linkage disequilibrium with the HindIII polymorphism of the DNF15S2 locus. Sequence analysis indicated that the DNF15S2 locus could potentially code for a previously unreported protein of 67 kDa which has 26 cysteine residues. DNF15S2 is part of the coding region of a 3.3-kb mRNA expressed in lung. Northern analysis indicated that this mRNA was not detectable in one of five SCLC lines. This SCLC line, H128, also lacks the enzyme aminoacylase 1.     

Containing Ontario's hospital costs under universal insurance in the 1980s: what was the record?

In recent years the Ontario government has been concerned that the proportion of public expenditures devoted to health care is at an all-time high. In addition, the media have devoted considerable attention to specific incidents that may represent inadequate funding of hospital services. To shed light on the debate on health care expenditures we analysed the trend in expenditures of Ontario''s hospital sector in the 1980s in terms of the amount of inputs (e.g., labour) used to produce hospital services (e.g., a patient-day or admission) and after adjustment for general inflation. As in the 1970s the number of inputs grew relatively slowly during the 1980s. Inputs per patient-day grew at an annual rate of 0.46% and inputs per admission at an annual rate of 2.4%. Cost increases were largely accounted for by hospital wage increases; this could have been due to Ontario''s rapidly expanding economy. These findings indicate that Ontario has continued to be successful in containing the number of inputs used in the hospital sector. However, after two decades of substantial success with publicly acceptable cost control, the government faces increased scrutiny as the media and the public focus attention on several areas of perceived inadequate funding in health care services.     

Partial Purification and Properties of Ornithine Transcarbamoylase from Nostoc muscorum Kützing

Ornithine transcarbamoylase (carbamoyl phosphate:l-ornithine carbamoyltransferase, EC 2.1.3.3) has been partially purified from the blue-green alga Nostoc muscorum Kützing, an organism in which the enzyme seems to be involved in a bicarbonate-fixing pathway leading to citrulline. Pertinent to possible regulation of this pathway, the enzyme shows hyperbolic substrate kinetics, has a molecular weight estimated at 75,000 daltons, and its catalytic capability is little influenced by a selection of metabolites that might conceivably act as regulators in vivo. Thus it seems unlikely that this enzyme is the control point for bicarbonate fixation. In terms of energy of activation (12.3 kcal/mole), size and Km for carbamoylphosphate, the Nostoc enzyme resembled preparations from liver and higher plants more than preparations from Streptococcus and Mycoplasma. The enzymes from Streptococcus and Mycoplasma are probably specialized for citrulline breakdown rather than citrulline synthesis. The Km for ornithine was 2.5 mm at a saturating concentration of carbamoylphosphate and the Km for carbamoylphosphate was 0.7 mm at an ornithine concentration of 2 mm. Ornithine was inhibitory at concentrations greater than 2 mm. Phosphate was a competitive inhibitor with respect to carbamoylphosphate. The pH optimum for citrulline synthesis was 9.5.     

The role of cytokinins in chloroplast lamellar development

The accumulation of chlorophyll, production of two specific lamellar chlorophyll-protein complexes, onset of O(2) evolution, and detection of P700 were examined in intact Jack bean (Canavalia ensiformis [L.] D.C.) leaves treated with 10(-5)m kinetin or benzyladenine and allowed to green under low (30-35%) and high (80-85%) relative humidity. In contrast to reports of the promotion of chlorophyll accumulation by cytokinin treatment in excised tissue or cotyledons, intact greening leaves showed neither promotion of chlorophyll accumulation nor alteration in formation of the lamellar chlorophyll-protein complexes or development of photosynthetic function. Furthermore, cytokinin was ineffective in relieving the consequences of low relative humidity water stress on chlorophyll accumulation and on the formation of at least one lamellar chlorophyll-protein.     

Activity rhythms in some burrowing decapods

Summary 1. Emphasis is placed upon the need for in situ observations on marine animals when designing actographs for laboratory recording of locomotor rhythmicity and when interpreting the adaptive value of such rhythmicity.2. Two burrowing decapods,Goneplax rhomboides andNephrops norvegicus, show highly persistent circadian rhythms when kept in actographs incorporating simulated burrows.3. In some other crustaceans interactions between individuals affect the period and amplitude of the spontaneous locomotor rhythm.4. The significance of very persistent rhythms in burrowing species is discussed.

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Aktivitätsrhythmen bei einigen höhlengrabenden Decapoden

Kurzfassung Es wird dargelegt, daß Untersuchungen über rhythmische Erscheinungen mariner Tiere ergänzender In-situ-Beobachtungen bedürfen, um die biologische Bedeutung von Periodizitätsphänomenen möglichst zweifelsfrei interpretieren zu können. Circadiane Rhythmen treten bei höhlengrabenden Decapoden deutlicher hervor, wenn den Versuchstieren künstliche Schlupfwinkel geboten werden, wie durch Aktivitätsregistrierungen anGoneplax rhomboides undNephrops norvegicus unter zeitgeberfreien Laboratoriumsbedingungen (bei konstantem Dämmerlicht) bewiesen werden konnte. Experimente anUca pugilator haben ergeben, daß die gezeitenrhythmische Lokomotionsperiodik durch soziale Kontakte beeinflußt wird. Bei größeren Gruppen wurde eine relativ geringere Aktivitätsmenge als bei kleineren Gruppen oder einzeln getesteten Individuen registriert. Die endogene Rhythmik höhlengrabender Decapoden erweist sich als außerordentlich persistent. Es wird erörtert, inwieweit dieser Persistenz eine adaptive Bedeutung zukommt.

     

Stress-induced cruciform formation in a cloned d(CATG)10 sequence.

The synthetic alternating purine-pyrimidine sequence, d(CATG)10.d(CATG)10, has been cloned into a 2.079-kb pBR322-derived plasmid (pLN1) and its conformation studied under torsional stress. The resultant plasmid, pLNc40, is hypersensitive to cleavage by the single strand-specific nucleases, S1 nuclease and Bal31 nuclease, and to modification by the single strand-selective reagent, osmium tetroxide. The S1-hypersensitive site of this plasmid predominates over those previously mapped in pBR322. Site-specific cleavage of pLNc40 with the resolvase T4 endonuclease VII demonstrates that this alternating purine-pyrimidine tract selectively forms a cruciform structure when stably integrated into a negatively supercoiled plasmid. Quantitative measurements of the twist change (-4.3 +/- 0.2) and free energy of formation (16.2 +/- 0.5 kcal/mol) of this cruciform have been made from two-dimensional gel electrophoresis experiments, and correspond well with the predicted values of cruciform formation for this sequence. We conclude that cruciform extrusion versus the B-Z transition is the favoured conformation of this insert under torsional stress.