High-level expression of the Endo-beta-N-acetylglucosaminidase F2 gene in E.coli: one step purification to homogeneity

The Endo F2gene was overexpressed in E.coli as a fusion protein joined to the maltose-binding protein. MBP-Endo F2was found in a highly enriched state as insoluble, inactive inclusion bodies. Extraction of the inclusion bodies with 20% acetic acid followed by exhaustive dialysis rendered the fusion protein active and soluble. MBP-Endo F2was digested with Factor Xaand purified on Q-Sepharose. The enzyme was homogeneous by SDS-PAGE, and appeared as a single symmetrical peak on HPLC. Analysis of the amino-terminus demonstrated conclusively that recombinant Endo F2was homogeneous and identical to the native enzyme.      

Development of highly selective fluorescent ferrocenyl-iminopyridine chemosensor for biologically relevant Fe3+

Design, synthesis, characterization, and ion detection studies of two ferrocene-appended Schiff bases namely N-(2-[ferrocenylamino]ethyl)-5-nitropyridin-2-amine ( 1 ) and ferrocenylamino-1H-imidazole-4-carboxamide ( 2 ) been reported. Both the chemosensors have been thoroughly characterized using Fourier transfer infrared, ¹H and ¹³C nuclear magnetic resonance, high resolution mass spectrometry, and ultraviolet/visible (UV/visible) and fluorescence spectral techniques. Probes 1 and 2 were designed with the aim of appending the ferrocenyl group with pyridine ring having an amine substitution (for 1 ) and imidazole ring with an amide substitution (for 2 ). Interaction of these probes with a series of cations and anions was examined through UV/vis and fluorescence spectral techniques. Probe 2 exhibited an insignificant response towards anions and loss of selectivity for cations, whereas 1 displayed highly selective detection towards biologically important Fe³⁺ in 2:1 (probe:cation) stoichiometry. Notably, none of the cations and anions could interfere the selectivity of Fe³⁺ ensured by 1 in aqueous medium. The limit of detection for Fe³⁺ detection using 1 was determined to be 0.2 ppm. The results strongly suggest that 1 could find promising future application as a chemosensor for Fe³⁺ in biological systems for quantification and qualitative analysis.     

The zero-sum assumption in neutral biodiversity theory

The neutral theory of biodiversity as put forward by Hubbell in his 2001 monograph has received much criticism for its unrealistic simplifying assumptions. These are the assumptions of functional equivalence among different species (neutrality), the assumption of point mutation speciation, and the assumption that resources are continuously saturated, such that constant resource availability implies constant community size (zero-sum assumption). Here we focus on the zero-sum assumption. We present a general theory for calculating the probability of observing a particular species-abundance distribution (sampling formula) and show that zero-sum and non-zero-sum formulations of neutral theory have exactly the same sampling formula when the community is in equilibrium. Moreover, for the non-zero-sum community the sampling formula has this same form, even out of equilibrium. Therefore, the term "zero-sum multinomial (ZSM)" to describe species abundance patterns, as coined by Hubbell [2001. The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ], is not really appropriate, as it also applies to non-zero-sum communities. Instead we propose the term "dispersal-limited multinomial (DLM)", thus making explicit one of the most important contributions of neutral community theory, the emphasis on dispersal limitation as a dominant factor in determining species abundances.     

Modes of speciation and the neutral theory of biodiversity

Hubbell's neutral theory of biodiversity has generated much debate over the need for niches to explain biodiversity patterns. Discussion of the theory has focused on its neutrality assumption, i.e. the functional equivalence of species in competition and dispersal. Almost no attention has been paid to another critical aspect of the theory, the assumptions on the nature of the speciation process. In the standard version of the neutral theory each individual has a fixed probability to speciate. Hence, the speciation rate of a species is directly proportional to its abundance in the metacommunity. We argue that this assumption is not realistic for most speciation modes because speciation is an emergent property of complex processes at larger spatial and temporal scales and, consequently, speciation rate can either increase or decrease with abundance. Accordingly, the assumption that speciation rate is independent of abundance (each species has a fixed probability to speciate) is a more natural starting point in a neutral theory of biodiversity. Here we present a neutral model based on this assumption and we confront this new model to 20 large data sets of tree communities, expecting the new model to fit the data better than Hubbell's original model. We find, however, that the data sets are much better fitted by Hubbell's original model. This implies that species abundance data can discriminate between different modes of speciation, or, stated otherwise, that the mode of speciation has a large impact on the species abundance distribution. Our model analysis points out new ways to study how biodiversity patterns are shaped by the interplay between evolutionary processes (speciation, extinction) and ecological processes (competition, dispersal).     

Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

Species abundance distributions (SADs) follow one of ecology's oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.     

Independent and competing disease risks: implications for host populations in variable environments

Disease models usually assume disease to act independently of other mortality- and morbidity-causing factors. Alternatively, disease may function as a competing risk factor, for example, killing already moribund hosts. Using tuberculosis (TB) in African buffalo as a model system, we explore consequences of competing or independent disease effects for host population dynamics. We include scenarios with density-dependent and density-independent effects of environmental variation, exemplified by variable food availability (driven by rainfall) and catastrophic droughts, respectively. Independent disease effects reduce population size linearly with prevalence, irrespective of the nature of environmental variation. Competing disease risks alter population size only if density-independent variation is present; then, disease reduces population size nonlinearly. Field data indicate that the net effect of TB on buffalo likely falls between the extremes of total independence and competition with other risk factors: TB increases mortality and decreases fecundity in some prime-aged buffalo, suggesting independent disease risks in these individuals, while similar disease effects in senescent buffalo may act as competing risks. Moreover, increased survival and fecundity of TB-negative buffalo may compensate for some disease-related losses. Model assumptions on independent or competing disease risks and environmental variability should be considered explicitly when assessing disease effects on wildlife populations.     

Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1

There are 10 gene families that have members on both human chromosome 6 (6p21.3, the location of the human major histocompatibility complex [MHC]) and human chromosome 9 (mostly 9q33-34). Six of these families also have members on mouse chromosome 17 (the mouse MHC chromosome) and mouse chromosome 2. In addition, four of these families have members on human chromosome 1 (1q21-25 and 1p13), and two of these have members on mouse chromosome 1. One hypothesis to explain these patterns is that members of the 10 gene families of human chromosomes 6 and 9 were duplicated simultaneously as a result of polyploidization or duplication of a chromosome segment ("block duplication"). A subsequent block duplication has been proposed to account for the presence of representatives of four of these families on human chromosome 1. Phylogenetic analyses of the 9 gene families for which data were available decisively rejected the hypothesis of block duplication as an overall explanation of these patterns. Three to five of the genes on human chromosomes 6 and 9 probably duplicated simultaneously early in vertebrate history, prior to the divergence of jawed and jawless vertebrates, and shortly after that, all four of the genes on chromosomes 1 and 9 probably duplicated as a block. However, the other genes duplicated at different times scattered over at least 1.6 billion years. Since the occurrence of these clusters of related genes cannot be explained by block duplication, one alternative explanation is that they cluster together because of shared functional characteristics relating to expression patterns.      

Coordination polymers and monomers based on new aminocarboxylate ligands: A cadmium(II) polymer containing dimeric aqua-bridged cadmium complex governed by polymeric chain

The synthesis and characterization of novel coordination polymers [Co(HCCB)(H₂O)₂]_n (1), [Zn(HCCB)(H₂O)₂]_n (2), {[Cd(HCCB)₂]·0.5[Cd(μ-H₂O)(H₂O)₄]₂}_n (3) and [Cu(HCCB)(H₂O)₂]_n (4) based on 3-(carboxymethylamino)-4-chlorobenzoic acid (H₃CCB) and mononuclear complexes [Cu(HBCCB)(H₂O)]·H₂O (5), [Co(HBCCB)(H₂O)]·H₂O (6), [Zn(HBCCB)(H₂O)] (7) and [Cd(HBCCB)(H₂O)] (8) containing 3-bis(carboxymethylamino)-4-chlorobenzoic acid (H₃BCCB) have been described. The compounds under investigation have been characterized by elemental analyses, spectral studies and structures of 1-3 and 5 determined crystallographically. Structural data of 1 and 2 revealed that the deprotonated HCCB²⁻ bridges metal centers leading to a double stranded 1D chain. On the other hand, the HCCB²⁻ coordinated thorough carboxylate oxygen and amino nitrogen in 3 to afford a 1D chain whose charge neutrality is maintained by inclusion of aqua-bridged dimer [{Cd(μ-H₂O)(H₂O)₄}₂]⁴⁺. Strong Cu?Cl interaction (2.754 Å) in 5 imposes a coordination geometry that is half-way between the square planar and square pyramidal. The H₃CCB, H₃BCCB and 1-3 and 5 are fluorescent at rt. Thermal studies (TG and DSC) on 1-3 suggested higher stability of 2 relative to 1 and 3 [ΔH_f (kcal/mol), ΔS_f = 152.17, 0.60, 1; 195.56: 0.86, 2; 69.33:0.36, 3].