Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes

Previous studies of the intertidal copepod Tigriopus californicus revealed one of the highest levels of mitochondrial DNA differentiation ever reported among conspecific populations. The present study extends the geographical sampling northward, adding populations from northern California to south-east Alaska. The mitochondrial phylogeny for the entire species range, based on cytochrome oxidase I sequences for a total of 49 individuals from 27 populations, again shows extreme differentiation among populations (up to 23%). However, populations from Oregon northwards appear to be derived and have interpopulation divergences five times lower than those between southern populations. Furthermore, although few individuals were sequenced from each locality, populations from Puget Sound northward had significantly reduced levels of within-population variation. These patterns are hypothesized to result from the contraction and expansion of populations driven by recent ice ages.     

Biodeterioration of natural stone with special reference to nitrifying bacteria

An evaluation of field data from historical buildings in Germany showed that chemoorganotrophic bacteria are the most numerous microorganisms in building stones, followed by fungi and nitrifying bacteria. Chemoorganotrophic bacteria and fungi were present in almost every sample. Ammonia and nitrite oxidizers were found in 55 and 62% of the samples, respectively. Within months, natural stone was colonized by chemoorganotrophic microorganisms. The highest cell numbers were usually found near the surface. The colonization of natural stone by nitrifying bacteria took several years. The highest cell numbers were in some cases found underneath the surface. Nitrifying bacteria showed a preference for calcareous material with a medium pore radius between 1 and 10 m. Cell numbers of nitrifying bacteria did not correlate to the nitrate content of the stone material. We demonstrated that the stone inhabiting microflora can cause significant loss of nitrate by denitrification. Our data strongly suggested that microbial colonization of historical buildings was enhanced by anthropogenic air pollution. Samples taken from stone material with a pore radius 1 m had significantly higher cell numbers when they were covered with black crusts. A comparison of samples taken between 1990–1995 from buildings throughout Germany showed that in eastern Germany a significantly stronger colonization with facultatively methylotrophic bacteria and nitrifying bacteria existed. The same was true for natural stone from an urban exposure site when compared to material from a rural exposure site. Data from outdoor exposure and laboratory simulation experiments indicated that the colonization of calcareous stone by nitrifying bacteria was enhanced by chemical weathering.     

The physical characteristics and usage patterns of stone axe and pounding hammers used by long‐tailed macaques in the Andaman Sea region of Thailand

Stone hammering in natural conditions has been extensively investigated in chimpanzees and bearded capuchins. In contrast, knowledge of stone tool use in wild Old World monkeys has been limited to anecdotal reports, despite having known for over 120 years that Macaca fascicularis aurea use stone tools to process shelled foods from intertidal zones on islands in the Andaman Sea. Our report is the first scientific investigation to look at the stone tools used by these macaques. We observed they were skilled tool users and used stone tools daily. They selected tools with differing qualities for differing food items, and appeared to use at least two types of stone tools. Pounding hammers were used to crush shellfish and nuts on anvils and axe hammers were used to pick or chip at oysters attached to boulders or trees. We found significant physical differences between these two tools. Tools at oyster beds were smaller and exhibited scarring patterns focused more often on the points, whereas tools found at anvils were larger and showed more scarring on the broader surfaces. We also observed grip differences between the two tool types. Lastly, macaques struck targets with axe hammers more rapidly and over a wider range of motion than with pounding hammers. Both our behavioral and lithic data support that axe hammers might be used with greater control and precision than pounding hammers. Hand‐sized axe hammers were used for controlled chipping to crack attached oysters, and larger pounding hammers were used to crush nuts and unattached shellfish on anvils. In addition to stones, they also used hand‐sized auger shells (Turritella attenuata) as picks to axe attached oysters. Pound hammering appears similar to the stone tools used by chimpanzees and capuchins, but axe hammering has not yet been documented in other nonhuman primates in natural conditions. Am. J. Primatol. 71:594–608, 2009. © 2009 Wiley‐Liss, Inc.     

微通道经皮肾镜取石术和标准通道经皮肾镜取石术的临床对比研究

目的：比较微通道经皮肾镜取石术和标准通道经皮肾镜取石术的临床效果。方法：选取2010 年1 月至2014 年5 月我院收 治的118 例肾结石患者,根据治疗方案分为微通道经皮肾镜取石术（MPCNL）（M 组,62 例）和标准通道经皮肾镜取石术（SPCNL） （S组,56 例）,比较两组术中术后相关指标和并发症情况。结果：与S 组相比,M组的手术时间更长,冲水量更多,但手术中出血量 更少,差异有统计学意义（P<0.05）;M 组术后血肌酐(Scr)、住院时间、卧床时间以及术后费用均小于或短于S 组,差异有统计学意 义（P<0.05）;两组结石清除率没有显著差异（P>0.05）;两组术后发热、出血、介入栓塞、结合穿孔、脓毒血症等并发症比较差异无统 计学意义（P>0.05）。结论：行MPCNL患者相比行SPCNL患者术后效果更好,临床上可根据结石的大小选择手术类型。     

Monte Carlo integration over stepping stone models for spatial genetic inference using approximate Bayesian computation

Approximate Bayesian computation (ABC) substitutes simulation for analytic models in Bayesian inference. Simulating evolutionary scenarios under Kimura’s stepping stone model (KSS) might therefore allow inference over spatial genetic process where analytical results are difficult to obtain. ABC first creates a reference set of simulations and would proceed by comparing summary statistics over KSS simulations to summary statistics from localities sampled in the field, but: comparison of which localities and stepping stones? Identical stepping stones can be arranged so two localities fall in the same stepping stone, nearest or diagonal neighbours, or without contact. None is intrinsically correct, yet some choice must be made and this affects inference. We explore a Bayesian strategy for mapping field observations onto discrete stepping stones. We make Sundial, for projecting field data onto the plane, available. We generalize KSS over regular tilings of the plane. We show Bayesian averaging over the mapping between a continuous field area and discrete stepping stones improves the fit between KSS and isolation by distance expectations. We make Tiler Durden available for carrying out this Bayesian averaging. We describe a novel parameterization of KSS based on Wright’s neighbourhood size, placing an upper bound on the geographic area represented by a stepping stone and make it available as m Vector. We generalize spatial coalescence recursions to continuous and discrete space cases and use these to numerically solve for KSS coalescence previously examined only using simulation. We thus provide applied and analytical resources for comparison of stepping stone simulations with field observations.     

Identification of parasite DNA in common bile duct stones by PCR and DNA sequencing

We attempted to identify parasite DNA in the biliary stones of humans via PCR and DNA sequencing. Genomic DNA was isolated from each of 15 common bile duct (CBD) stones and 5 gallbladder (GB) stones. The patients who had the CBD stones suffered from cholangitis, and the patients with GB stones showed acute cholecystitis, respectively. The 28S and 18S rDNA genes were amplified successfully from 3 and/or 1 common bile duct stone samples, and then cloned and sequenced. The 28S and 18S rDNA sequences were highly conserved among isolates. Identity of the obtained 28S D1 rDNA with that of Clonorchis sinensis was higher than 97.6%, and identity of the 18S rDNA with that of other Ascarididae was 97.9%. Almost no intra-specific variations were detected in the 28S and 18S rDNA with the exception of a few nucleotide variations, i.e., substitution and deletion. These findings suggest that C. sinensis and Ascaris lumbricoides may be related with the biliary stone formation and development.     

Stone-tool usage by Thai long-tailed macaques (Macaca fascicularis)

In January and March of 2005, we conducted surveys of long-tailed macaques at Piak Nam Yai Island, Laem Son National Park (9 degrees N 34-35', 98 degrees E 28'), Ranong Province, situated in southern Thailand. Two of the three troops of long-tailed macaques found on the island were observed using axe-shaped stones to crack rock oysters, detached gastropods (Thais tissoti, Petit, 1852), bivalves (Gafrarium divaricatum, Gmelin, 1791), and swimming crabs (Thalamita danae, Stimpson, 1858). They smashed the shells with stones that were held in either the left or right hand, while using the opposite hand to gather the oyster meat. Some monkeys used both hands to handle the stones. According to Matsuzawa's 1996 hierarchical classification of tool usage (levels 0-3), the tool usage by Thai long-tailed macaques could be characterized as either level 1 (cracking rock oysters with stones) or level 2 (cracking drifting mollusks and crabs with stones by placing them on a rock). Our discovery of stone-tool usage by Thai long-tailed macaques provides a new point of reference for discussions regarding the evolution of tool usage and the material culture of primates.     

Limiting processes for perennial plant reintroduction to restore dry grasslands

In restored grasslands of southern Europe, perennial plants remain highly underrepresented compared with the reference ecosystems. We tested various treatments to reintroduce common perennial plant species (Brachypodium retusum, Poaceae, and Thymus vulgaris, Lamiaceae), which are usually not or poorly reintroduced via soil and hay transfer. Treatments included microenvironmental manipulations (rock cover and plant interactions) and two grazing intensities. Target perennial species were transplanted in 2002 in the reference grassland ecosystem (intact grassland area used as a control) and in two abandoned fields. Survival was assessed in June 2003 and June 2004. Target species shoot and root biomass were measured in June 2004. Grazing greatly reduced the survival and biomass of both target species and its effects were reinforced by summer drought: plants that did not establish well enough during the autumn and spring did not survive summer. The restored rock cover had a mild positive effect, particularly on B. retusum. There were no negative or positive plant neighbor interactions in the steppe, while there was competition in both abandoned fields. Competition was particularly intense in the abandoned melon field, composed of a dense sward of annual grasses (Bromus sp.). In order to reintroduce perennial species to dry grasslands, the ideal combination of treatments is to exclude or reduce grazing during the first year to allow seedlings to establish and to recreate adequate microenvironmental conditions. Reducing competition from arable weeds may help but is not essential in such dry grasslands.