Molecular evolution modeled as a fractal Poisson process in agreement with mammalian sequence comparisons

The fractal doubly stochastic Poisson process (FDSPP) model of molecular evolution, like other doubly stochastic Poisson models, agrees with the high estimates for the index of dispersion found from sequence comparisons. Unlike certain previous models, the FDSPP also predicts a positive geometric correlation between the index of dispersion and the mean number of substitutions. Such a relationship is statistically proven herein using comparisons between 49 mammalian genes. There is no characteristic rate associated with molecular evolution according to this model, but there is a scaling relationship in rates according to a fractal dimension of evolution. The FDSPP is a suitable replacement for the homogeneous Poisson process in tests of the lineage dependence of rates and in estimating confidence intervals for divergence times. As opposed to other fractal models, this model can be interpreted in terms of Darwinian selection and drift.      

Cloning in Bacillus subtilis of an extremely thermostable alpha amylase: comparison with other cloned heatstable alpha amylases

A heatstable alpha amylase gene was shotgun cloned from Bacillus licheniformis RPO1 into Bacillus subtilis. Restriction endonuclease analysis of the recombinant plasmid revealed a map which was identical to a previously cloned alpha amylase from B. licheniformis FDO2 and very similar to the restriction map of a high temperature amylase from Bacillus coagulans. The thermostability and temperature optimum of the cloned alpha amylase was measureably different from those of the previously reported cloned alpha amylases.     

Purification of multiple forms of adenosine deaminase from rabbit intestine.

Two forms of adenosine deaminase (adenosine aminohydrolase, EC 3.5.4.4), differing in molecular size, have been purified and obtained in homogeneous form from rabbit intestine. The purification procedures involved extraction with acetate buffer, pH 5.5, precipitation and fractional reextraction with (NH4)2SO4, ion-exchange chromatography on DEAE-cellulose and gel filtration on Sephadex G-75 and Sephadex G-200. Gel filtrations analysis gave molecular weight estimates of 265 000 and 32 000 for the large and small deaminases respectively. The two enzymes forms had similar pH optima and pH stability ranges.     

The effect of agriculture on the seasonal dynamics and functional diversity of benthic biofilm in tropical headwater streams

Tropical streams are one of the most endangered ecosystems in the world due to the constant pressures from human activities. Among these activities, agriculture represents a land use that is crucial for human development but also a key driver of stream degradation and biodiversity decline in the tropics. Against this background, we investigated indirect effects of agriculture (alterations in stream flow and nutrient availability) and climate characteristics (water temperature) on benthic biofilm communities in tropical streams (São Paulo State, Brazil). Three first‐order streams draining catchments dominated by agricultural land use (sugarcane for bioenergy production, pasture) with some remaining riparian forest were studied for 1 year. We focused on the relationships of benthic biofilm biomass, algal biomass, diatom community, and functional structure with streamflow dynamics, nitrate concentrations, and water temperature. Our results indicate that these biological responses were mainly mediated by flow and water temperature and not by resource availability in the studied headwater streams. This result could be explained by the heavy rains and elevated runoff generation in these tropical catchments under agricultural influence, which might override the known effects of nutrient enrichment on benthic biofilm communities. Considering forecast climate and land‐use changes in tropical streams, our findings may suggest potential shifts in benthic biofilm communities, with functional consequences for aquatic food webs in these environments. Abstract in Brazilian Portuguese is available with online material.     

Caenorhabditis elegans junctophilin has tissue-specific functions and regulates neurotransmission with extended-synaptotagmin

The junctophilin family of proteins tether together plasma membrane (PM) and endoplasmic reticulum (ER) membranes, and couple PM- and ER-localized calcium channels. Understanding in vivo functions of junctophilins is of great interest for dissecting the physiological roles of ER-PM contact sites. Here, we show that the sole Caenorhabditis elegans junctophilin JPH-1 localizes to discrete membrane contact sites in neurons and muscles and has important tissue-specific functions. jph-1 null mutants display slow growth and development due to weaker contraction of pharyngeal muscles, leading to reduced feeding. In the body wall muscle, JPH-1 colocalizes with the PM-localized EGL-19 voltage-gated calcium channel and ER-localized UNC-68 RyR calcium channel, and is required for animal movement. In neurons, JPH-1 colocalizes with the membrane contact site protein Extended-SYnaptoTagmin 2 (ESYT-2) in the soma, and is present near presynaptic release sites. Interestingly, jph-1 and esyt-2 null mutants display mutual suppression in their response to aldicarb, suggesting that JPH-1 and ESYT-2 have antagonistic roles in neuromuscular synaptic transmission. Additionally, we find an unexpected cell nonautonomous effect of jph-1 in axon regrowth after injury. Genetic double mutant analysis suggests that jph-1 functions in overlapping pathways with two PM-localized voltage-gated calcium channels, egl-19 and unc-2, and with unc-68 for animal health and development. Finally, we show that jph-1 regulates the colocalization of EGL-19 and UNC-68 and that unc-68 is required for JPH-1 localization to ER-PM puncta. Our data demonstrate important roles for junctophilin in cellular physiology, and also provide insights into how junctophilin functions together with other calcium channels in vivo.     

Bill morphology reflects adaptation to a fibrous diet in the kākāpō (Strigops: Psittaciformes)

We describe the upper portion of the bill sheath (rhinotheca) of the kākāpō (Strigops habroptilus) from three adult female specimens. The external buccal surface of the rhinotheca is deeply concave with a prominent palatal stop and hardened chevrons creating a ‘milling apparatus’ that the kākāpō uses to grind food. The palatal stop presents a working face of 40–50?mm². The internal surface of the rhinotheca mirrors the overlying premaxilla and provides a distinct thickened abutment consistent with resistance against the increased workload of the mandibles (gnathotheca) due to the kākāpō’s fibrous diet and chewing style. Along the midline, the rhinotheca at the abutment is up to 5.6?mm thick, compared with as thin as 2.1?mm elsewhere on the midline. The closely related Nestor parrots have less developed palatal stops, chevrons and abutments on their rhinothecas consistent with their lower preference for fibrous plant material. The form of the rhinotheca agrees with the kākāpō’s feeding ecology as a generalist herbivore that grinds locally available fibrous material to assist digestion.     

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.     

Effects of Hunting on Response Behaviors of Wild Reindeer

ABSTRACT Because wild reindeer (Rangifer tarandus) are hunted in southern Norway, reindeer may perceive all recreationists as threats. Potential adverse effects of hunting on reindeer behavior may be exacerbated by other forms of recreation because the number of skiers and hikers in areas inhabited by reindeer has also increased. The Norefjell-Reinsjøfjell wild reindeer area is used extensively for recreation and tourism. Reindeer hunting was introduced in the area in 1992, and harvest rate has been stable at about 38% of winter herd size. We recorded behavioral responses of reindeer to a person approaching directly on foot or skis during 1992 and again in 2002–2006. Compared to 1992, flight-initiation distance increased and fewer groups assessed the observer before taking flight during 2002–2006. In winter, when reindeer are usually comparably more vigilant than in other seasons, flight-initiation distance increased from only 60 m to 115 m and escape distance decreased from 400 m to 210 m. Neither alert distance, calf carcass weights (23.6 ± 0.7 [SE] kg to 22.4 ± 0.2 kg), nor reindeer herd size (661 ± 73 to 579 ± 15) changed during the 15 years of our study. Reindeer appeared to habituate to the observer because they initiated flight at shorter distances as the number of approaches on the same day increased. In Norefjell-Reinsjøfjell, encounters with a person on foot or skis did not result in behavioral responses likely to entail substantial energy costs for reindeer; therefore, hunting at current levels appears compatible with other recreational activities.     

A study of fungi found in association with Histoplasma capsulatum: three bird roosts in S.E. Missouri,U.S.A.

Summary Soil samples from three bird roosts in SE Missouri were studied in an effort to detect differences in the distribution of microfungi in sites contaminated withHistoplasma capsulatum and presumably favorable, but uncontaminated sites. Seventy-four of 151 species identified were found in conjunction withH. capsulatum; many of the remaining 77 species were isolated only rarely and are probably not important colonizers of these soils. Only minor differences were noted regarding distribution of more commonly occurring species. Fungi known to be parasitic or antagonistic to other microfungi were about evenly distributed among the sites.H. capsulatum was most abundant in the one roost which was still occupied by flocks of birds.