Breeding ecology of the endemic Black Lark <Emphasis Type="Italic">Melanocorypha yeltoniensis</Emphasis> on natural steppe and abandoned croplands in post-Soviet Kazakhstan

Since the collapse of the Soviet Union in 1991, the abundance and distribution of many central Asian steppe birds have been affected by changes in agricultural land management, such as the abandonment of large areas of cropland and changing grazing patterns. However, the underlying population processes that drive patterns of abundance and distribution are poorly understood. We compared the population ecology of the Black Lark Melanocorypha yeltoniensis on natural steppe and abandoned cropland. Between 2009 and 2013, we used distance sampling to quantify Black Lark population density, monitored 220 nests to assess reproductive performance, and modelled habitat selection at several scales. Arthropod food availability was compared using pitfall traps. Mean population densities were three times higher on abandoned cropland compared to those in steppe, and varied with time since abandonment. Nest survival rates were significantly lower on abandoned cropland compared to steppe, probably due to higher predation pressure. Chick growth rates were also lower on abandoned cropland, despite higher insect availability in this habitat. Habitat selection was strongly influenced by grazing intensity and vegetation structure. We suggest that Black Larks are generally attracted to abandoned cropland because of its suitable vegetation structure and higher food availability. The results of a fecundity model suggested that the number of breeding attempts on abandoned cropland necessary to produce the same number of fledglings as one nesting attempt in steppe habitat was 2.04 in 2011 and 3.62 in 2013. However, a phenological analysis revealed that there were only two peaks in first egg dates, making more than two re-nesting attempts per year unlikely. Therefore, abandoned cropland could, at least in some years, be an ecological trap for the species. Our results illustrate that the effects of land-use change on animal populations should not only be assessed using species densities, but also incorporate detailed demographic analyses. If current densities in steppe habitat corresponded to maximum carrying capacity, overall population densities of Black Larks are likely to decline in the near future as availability of abandoned cropland as nesting habitat is currently decreasing.     

Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor.

Human growth hormone (hGH) binds to its receptor (hGHr) in a three-body interaction: one molecule of the hormone and two identical monomers of the receptor form a trimer. Curiously, the hormone-receptor interactions in the trimer are not equivalent and the formation of the complex occurs in a specific kinetic order (Cunningham BC, Ultsch M, De Vos AM, Mulkerrin MG, Clauser KR, Wells JA, 1991, Science 254:821-825). In this paper, we model the recognition of hGH to the hGHr using shape complementarity of the three-dimensional structures and macromolecular docking to explore possible binding modes between the receptor and hormone. The method, reported previously (Hendrix DK, Kuntz ID, 1998, Pacific symposium on biocomputing 1998, pp 1234-1244), is based upon matching complementary-shaped strategic sites on the molecular surface. We modify the procedure to examine three-body systems. We find that the order of binding seen experimentally is also essential to our model. We explore the use of mutational data available for hGH to guide our model. In addition to docking hGH to the hGHr, we further test our methodology by successfully reproducing 16 macromolecular complexes from X-ray crystal structures, including enzyme-inhibitor, antibody-antigen, protein dimer, and protein-DNA complexes.     

Distinct regulation of pHin and [Ca2+]in in human melanoma cells with different metastatic potential

We investigated whether alterations in the mechanisms involved in intracellular pH (pHⁱⁿ) and intracellular calcium ([Ca²⁺]ⁱⁿ) homeostasis are associated with the metastatic potential of poorly (A375P) and highly (C8161) metastatic human melanoma cells. We monitored pHⁱⁿ and [Ca²⁺]ⁱⁿ simultaneously, using the fluorescence of SNARF-1 and Fura-2, respectively. Our results indicated that steady-state pHⁱⁿ and [Ca²⁺]ⁱⁿ between these cell types were not significantly different. Treatment of cells with NH₄Cl resulted in larger pHⁱⁿ increases in highly than in poorly metastatic cells, suggesting that C8161 cells have a lower H⁺ buffering capacity than A375P. NH₄Cl treatment also increased [Ca²⁺]ⁱⁿ only in C8161 cells. To determine if the changes in [Ca²⁺]ⁱⁿ triggered by NH₄Cl treatment were due to alterations in either H⁺- or Ca²⁺-buffering capacity, cells were treated with the Ca²⁺-ionophore 4Br-A23187, to alter [Ca²⁺]ⁱⁿ. The magnitude of the ionophore-induced [Ca²⁺]ⁱⁿ increase was slightly greater in C8161 cells than in A375P. Moreover, A375P cells recover from the ionophore-induced [Ca²⁺]ⁱⁿ load, whereas C8161 cells did not, suggesting that A375P may exhibit distinct [Ca²⁺]ⁱⁿ regulatory mechanisms than C8161 cells, to recover from Ca²⁺ loads. Removal of extracellular Ca²⁺ ([Ca²⁺]^ex) decreased [Ca²⁺]ⁱⁿ in both cell types at the same extent. Ionophore treatment in the absence of [Ca²⁺]^ex transiently increased [Ca²⁺]ⁱⁿ in C8161, but not in A375P cells. Endoplasmic reticulum (ER) Ca²⁺-ATPase inhibitors such as cyclopiazonic acid (CPA) and thapsigargin (TG) increased steady-state [Ca²⁺]ⁱⁿ only in C8161 cells. Together, these data suggest that the contribution of intracellular Ca²⁺ stores for [Ca²⁺]ⁱⁿ homeostasis is greater in highly than in poorly metastatic cells. Bafilomycin treatment, to inhibit V-type H⁺-ATPases, corroborated our previous results that V-H⁺-ATPases are functionally expressed at the plasma membranes of highly metastatic, but not in poorly metastatic cells in and [Ca²⁺]ⁱⁿ regulatory mechanisms are present in poorly and highly metastatic human melanoma cells. J. Cell. Physiol. 176:196–205, 1998. © 1998 Wiley-Liss, Inc.     

Butterfly, bee and forb community composition and cross-taxon incongruence in tallgrass prairie fragments

Pollinators provide an important class of ecological services for crop plants and native species in many ecosystems, including the tallgrass prairie, and their conservation is essential to sustaining prairie remnants. In Iowa these remnants are typically either block-shaped or long, linear strips along transportation routes. In this study we examined differences in the butterfly, bee, and forb community composition in linear and block prairie remnants, determined correlations between species diversity among butterflies, bees and forbs in the 20 prairie remnants sampled, and examined correlations of community similarity among butterflies, bees and forbs. Correspondence analysis showed that distinct communities exist for butterflies and forbs in block versus linear sites and discriminant analysis showed that the bee and forb communities in block and linear sites can be distinguished on the basis of a few species. Diversity of one group was a poor predictor of diversity in another, except for a significant inverse relationship between bees and butterflies. These two pollinator taxa may be responding very differently to microhabitat components within fragmented ecosystems. Our studies show that there need to be differences in conservation strategies for bees and butterflies to maintain both pollinator communities.     

HisE11 and HisF8 Provide Bis-histidyl Heme Hexa-coordination in the Globin Domain of Geobacter sulfurreducens Globin-coupled Sensor

Among heme-based sensors, recent phylogenomic and sequence analyses have identified 34 globin coupled sensors (GCS), to which an aerotactic or gene-regulating function has been tentatively ascribed. Here, the structural and biochemical characterization of the globin domain of the GCS from Geobacter sulfurreducens (GsGCS¹⁶²) is reported. A combination of X-ray crystallography (crystal structure at 1.5 Å resolution), UV-vis and resonance Raman spectroscopy reveals the ferric GsGCS¹⁶² as an example of bis-histidyl hexa-coordinated GCS. In contrast to the known hexa-coordinated globins, the distal heme-coordination in ferric GsGCS¹⁶² is provided by a His residue unexpectedly located at the E11 topological site. Furthermore, UV-vis and resonance Raman spectroscopy indicated that ferrous deoxygenated GsGCS¹⁶² is a penta-/hexa-coordinated mixture, and the heme hexa-to-penta-coordination transition does not represent a rate-limiting step for carbonylation kinetics. Lastly, electron paramagnetic resonance indicates that ferrous nitrosylated GsGCS¹⁶² is a penta-coordinated species, where the proximal HisF8-Fe bond is severed.     

Structure and Energetics of Encapsidated DNA in Bacteriophage HK97 Studied by Scanning Calorimetry and Cryo-electron Microscopy

Encapsidation of duplex DNA by bacteriophages represents an extreme case of genome condensation, reaching near-crystalline concentrations of DNA. The HK97 system is well suited to study this phenomenon in view of the detailed knowledge of its capsid structure. To characterize the interactions involved, we combined calorimetry with cryo-electron microscopy and native gel electrophoresis. We found that, as in other phages, HK97 DNA is organized in coaxially wound nested shells. When DNA-filled capsids (heads) are scanned in buffer containing 1 mM Mg²⁺, DNA melting and capsid denaturation both contribute to the complex thermal profile between 82 °C and 96 °C. In other conditions (absence of Mg²⁺ and lower ionic strength), DNA melting shifts to lower temperatures and the two events are resolved. Heads release their DNA at temperatures well below the onset of DNA melting or capsid denaturation. We suggest that, on heating, the internal pressure increases, causing the DNA to exit—probably via the portal vertex-while the capsid, although largely intact, sustains local damage that leads to an earlier onset of thermal denaturation. Heads differ structurally from empty capsids in the curvature of their protein shell, a change attributable to outwards pressure exerted by the DNA. We propose that this transition is sensed by the portal that is embedded in the capsid wall, whereupon the structure of the portal and its interactions with terminase, the packaging enzyme, are altered, thus signaling that packaging is at or approaching completion.     

A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in upland cotton (Gossypium hirsutum L.)

An F_4:5 population of 285 families with each tracing back to a different F₂ plant, derived from a cotton bacterial blight resistant line ‘DeltaOpal’ and a susceptible line ‘DP388’, was artificially inoculated with bacterial blight race 18 (Xanthomonas axonopodis pv. malvacearum) to assay their resistance or susceptibility to the disease. The segregation in the F_4:5 population indicates that the resistance was conditioned by a single dominant gene designated B _12. Simple sequence repeat (SSR) markers identified as putatively linked to the resistance gene by bulked segregant analysis were confirmed on the entire F_4:5 population. Three SSR markers, CIR246, BNL3545 and BNL3644 on chromosome 14, were found closely linked to B ₁₂ . The association between CIR246 and B ₁₂ was validated among 354 plants of 16 diverse varieties. Based on Monsanto SSR/single nucleotide polymorphism (SNP) consensus map, SNP markers closely linked to CIR246 were used to screen ‘DeltaOpal’ and ‘DP388’ for polymorphism. The polymorphic SNP markers were run on the F_4:5 population and the four SNP markers spanning 3.4 cM were found to flank the resistance gene on chromosome 14. The linkage between B ₁₂ and the 4-SNP marker haplotype was validated using 18 elite cotton lines. This 4-SNP marker haplotype can be used for marker assisted selection for bacterial blight resistance breeding programs or for screening germplasm collections for this locus rapidly.     

FtsZ-less cell division in archaea and bacteria

A dedicated cell division machinery is needed for efficient proliferation of an organism. The eukaryotic actin-myosin based mechanism and the bacterial FtsZ-dependent machinery have both been characterized in detail, and a third division mechanism, the Cdv system, was recently discovered in archaea from the Crenarchaeota phylum. Despite these findings, division mechanisms remain to be identified in, for example, organisms belonging to the bacterial PVC superphylum, bacteria with extremely reduced genomes, wall-less archaea and bacteria, and in archaea that carry out the division process without cell constriction. Cytokinesis mechanisms in these clades and individual taxa are likely to include adaptation of host functions to division of bacterial symbionts, transfer of bacterial division genes into the host genome, vesicle formation without a dedicated constriction machinery, cross-wall formation without invagination, as well as entirely novel division mechanisms.     

Crosslinking in viral capsids via tiling theory

A vital part of a virus is its protein shell, called the viral capsid, that encapsulates and hence protects the viral genome. It has been shown in Twarock [2004. A tiling approach to vius capsids assembly explaining a structural puzzle in virology. J. Theor. Biol. 226, 477-482] that the surface structures of viruses with icosahedrally symmetric capsids can be modelled in terms of tilings that encode the locations of the protein subunits. This theory is extended here to multi-level tilings in order to model crosslinking structures. The new framework is demonstrated for the case of bacteriophage HK97, and it is shown, how the theory can be used in general to decide if crosslinking, and what type of crosslinking, is compatible from a mathematical point of view with the geometrical surface structure of a virus.