Genome wide interactions of wild-type and activator bypass forms of σ54

Enhancer-dependent transcription involving the promoter specificity factor σ54 is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ54-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since activators can be bypassed in vitro, bypass transcription in vivo could be a source of emergent gene expression along evolutionary pathways yielding new control networks and transcription patterns. At a single test promoter in vivo bypass transcription was not observed. We now use genome-wide transcription profiling, genome-wide mutagenesis and gene over-expression strategies in Escherichia coli, to (i) scope the range of bypass transcription in vivo and (ii) identify genes which might alter bypass transcription in vivo. We find little evidence for pervasive bypass transcription in vivo with only a small subset of σ54 promoters functioning without activators. Results also suggest no one gene limits bypass transcription in vivo, arguing bypass transcription is strongly kept in check. Promoter sequences subject to repression by σ54 were evident, indicating loss of rpoN (encoding σ54) rather than creating rpoN bypass alleles would be one evolutionary route for new gene expression patterns. Finally, cold-shock promoters showed unusual σ54-dependence in vivo not readily correlated with conventional σ54 binding-sites.

Control of wild rubber extraction in the forests of northeast India, 1850-1880

This paper uses the history of rubber extraction to explore competing attempts to control the forest environments of Assam and beyond in the second half of the nineteenth century. Forest communities faced rival efforts at environmental control from both European and Indian traders, as well as from various centres of authority within the Raj. Government attempts to regulate rubber collection were undermined by the weak authority of the Raj in these regions, leading to widespread smuggling. Partly in response to the disruptive influence of rubber traders on the frontier, the Raj began to restrict the presence of outsiders in tribal regions, which came to be understood as distinct areas outside British control. When rubber yields from the forests nearest the Brahmaputra fell in the wake of intensive exploitation, India's scientific foresters demanded and from 1870 obtained the ability to regulate the Assamese forests, blaming indigenous rubber tapping strategies for the declining yields and arguing that Indian rubber could be ‘equal [to] if not better' than Amazonian rubber if only tappers would change their practices. The knowledge of the scientific foresters was fundamentally flawed, however, and their efforts to establish a new type of tapping practice failed. By 1880, the government had largely abandoned attempts to regulate wild Indian rubber, though wild sources continued to dominate the supply of global rubber until after 1910.

A let-7 microRNA-binding site polymorphism in 3'-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy

PURPOSE: recent studies have found that KRAS mutations predict resistance to monoclonal antibodies targeting the epidermal growth factor receptor in metastatic colorectal cancer (mCRC). A polymorphism in a let-7 microRNA complementary site (lcs6) in the KRAS 3' untranslated region (UTR) is associated with an increased cancer risk in non-small-cell lung cancer and reduced overall survival (OS) in oral cancers. We tested the hypothesis whether this polymorphism may be associated with clinical outcome in KRAS wild-type (KRASwt) mCRC patients treated with cetuximab monotherapy.

PATIENTS AND METHODS: the presence of KRAS let-7 lcs6 polymorphism was evaluated in 130 mCRC patients who were enrolled in a phase II study of cetuximab monotherapy (IMCL-0144). Genomic DNA was extracted from dissected formalin-fixed paraffin-embedded tumor tissue, KRAS mutation status and polymorphism were assessed using direct sequencing and PCR restriction fragment length polymorphism technique.

RESULTS: KRAS let-7 lcs6 polymorphism was found to be related to object response rate (ORR) in mCRC patients whose tumors had KRASwt. The 12 KRASwt patients harboring at least a variant G allele (TG or GG) had a 42% ORR compared with a 9% ORR in 55 KRASwt patients with let-7 lcs6 TT genotype (P = 0.02, Fisher's exact test). KRASwt patients with TG/GG genotypes had trend of longer median progression-free survival (3.9 versus 1.3 months) and OS (10.7 versus 6.4 months) compared to those with TT genotypes.

CONCLUSIONS: these results are the first to indicate that the KRAS 3'UTR polymorphism may predict for cetuximab responsiveness in KRASwt mCRC patients, which warrants validation in other clinical trials.

Ecological differences and coexistence in a guild of microparasites: Bartonella in wild rodents

The study of ecological differences among coexisting microparasites has been largely neglected, but it addresses important and unusual issues because there is no clear distinction in such cases between conventional (resource) and apparent competition. Here patterns in the population dynamics are examined for four species of Bartonella (bacterial parasites) coexisting in two wild rodent hosts, bank voles (Clethrionomys glareolus) and wood mice (Apodemus sylvaticus). Using generalized linear modeling and mixed effects models, we examine, for these four species, seasonal patterns and dependencies on host density (both direct and delayed) and, having accounted for these, any differences in prevalence between the two hosts. Whereas previous studies had failed to uncover species differences, here all four were different. Two, B. doshiae and B. taylorii, were more prevalent in wood mice, and one, B. birtlesii, was more prevalent in bank voles. B. birtlesii, B. grahamii, and B. taylorii peaked in prevalence in the fall, whereas B. doshiae peaked in spring. For B. birtlesii in bank voles, density dependence was direct, but for B. taylorii in wood mice density dependence was delayed. B. birtlesii prevalence in wood mice was related to bank vole density. The implications of these differences for species coexistence are discussed.

The dynamics of murid gammaherpesvirus 4 within wild, sympatric populations of bank voles and wood mice

Murid gammaherpesvirus 4 (MuHV-4) is widely used as a small animal model for understanding gammaherpesvirus infections in man. However, there have been no epidemiological studies of the virus in wild populations of small mammals. As MuHV-4 both infects cells associated with the respiratory and immune systems and attempts to evade immune control via various molecular mechanisms, infection may reduce immunocompetence with potentially serious fitness consequences for individuals. Here we report a longitudinal study of antibody to MuHV-4 in a mixed assemblage of bank voles (Clethrionomys glareolus) and wood mice (Apodemus sylvaticus) in the UK. The study was conducted between April 2001 and March 2004. Seroprevalence was higher in wood mice than bank voles, supporting earlier work that suggested wood mice were the major host even though the virus was originally isolated from a bank vole. Analyses of both the probability of having antibodies and the probability of initial seroconversion indicated no clear seasonal pattern or relationship with host density. Instead, infection risk was most closely associated with individual characteristics, with heavier males having the highest risk. This may reflect individual variation in susceptibility, potentially related to variability in the ability to mount an effective immune response.

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Background: Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies. Methods: A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results. Results: Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the betweenand within-breed components of genetic diversity. Conclusions: Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.

Mad O'Hara of Wild River due date card

This is a due date card for the book titled Mad O'Hara of Wild River, with stamped dates from 1941.

An analysis of bimanual actions in natural feeding of semi-wild chimpanzees

Objective The objective of the current study was to investigate the lateral dominance for a bimanually coordinated natural feeding behavior in semi-wild chimpanzees. Materials and Methods We investigated strychnos spp. fruit consumption behaviors in semi-wild chimpanzees as an ecologically comparable feeding behavior to those found in cerebral lateralization studies of non-primate species. Video recordings of thirty-three chimpanzees were assessed while they consumed hard-shelled strychnos fruits. We explored statistical and descriptive measures of hand dominance to highlight lateralized patterns. Results Statistical evaluation of feeding bouts revealed a group-level right-handed bias for bimanual coordinated feeding actions, however few individuals were statistically lateralized. Descriptive analyses revealed that the majority of individuals were lateralized and possessed a right-handed bias for strychnos feeding behavior. Discussion The results provide empirical evidence in supports of an early evolutionary delineation of function for the right and left hemispheres. The present findings suggest that great apes express an intermediate stage along the phylogenetic trajectory of human manual lateralization.

Comparison of allocation approaches in soybean biodiesel life cycle assessment

This work shows the influence of using different allocation approaches when modelling the inventory analysis in a soybean biodiesel life cycle assessment (LCA). Results obtained using mass, energy and economic based allocations are compared, focusing on the following aspects: normalised potential environmental impact (PEI) categories, total PEI and relative contributions to the total PEI from each life cycle stage and environmental impact category. Similar results are obtained either using economic and energy based allocations. However, different results are obtained when mass based allocation is used when compared with the other two. This study also illustrates that using different allocation approaches in biodiesel LCA may influence the final conclusions, especially in comparative assertions, emphasising the need to perform a sensitivity analysis in the LCA interpretation step.

Cultural innovation and transmission of tool use in wild chimpanzees:evidence from field experiments

Animal Cognition, V.6, pp. 213-223

Distribution of the entodiniomorphid ciliate Troglocorys cava Tokiwa, Modrý, Ito, Pomajbíková, Petrželková, & Imai, , (Entodiniomorphida: Blepharocorythidae) in wild and captive chimpanzees.

Trophozoites of Troglocorys cava were detected in all but one of the wild chimpanzee populations from Rubondo Island (Tanzania), with a prevalence ranging between 20% and 78%. However, the ciliate was absent in all captive groups. Prevalence appeared to increase with the number of sequential samples taken from a particular individual and reached 95.5% in wild individuals sampled at least 4 times.

Seroprevalence of hepatitis e virus in domestic pigs and wild boars in Switzerland.

Hepatitis E is considered an emerging human viral disease in industrialized countries. Studies from Switzerland report a human seroprevalence of hepatitis E virus (HEV) of 2.6-21%, a range lower than in adjacent European countries. The aim of this study was to determine whether HEV seroprevalence in domestic pigs and wild boars is also lower in Switzerland and whether it is increasing and thus indicating that this zoonotic viral infection is emerging. Serum samples collected from 2,001 pigs in 2006 and 2011 and from 303 wild boars from 2008 to 2012 were analysed by ELISA for the presence of HEV-specific antibodies. Overall HEV seroprevalence was 58.1% in domestic pigs and 12.5% in wild boars. Prevalence in domestic pigs was significantly higher in 2006 than in 2011. In conclusion, HEV seroprevalence in domestic pigs and wild boars in Switzerland is comparable with the seroprevalence in other countries and not increasing. Therefore, prevalence of HEV in humans must be related to other factors than prevalence in pigs or wild boars.

Ecology and neurophysiology of sleep in two wild sloth species

Study Objectives: Interspecific variation in sleep measured in captivity correlates with various physiological and environmental factors, including estimates of predation risk in the wild. However, it remains unclear whether prior comparative studies have been confounded by the captive recording environment. Herein we examine the impact of predation pressure on sleep in sloths living in the wild. Design: Comparison of two closely related sloth species, one exposed to predation and one free from predation. Setting: Panamanian mainland rainforest (predators present) and island mangrove (predators absent). Participants: Mainland (Bradypus variegatus, 5 males and 4 females) and island (Bradypus pygmaeus, 6 males) sloths. Interventions: None. Measurements and Results: EEG and EMG activity were recorded using a miniature data logger. Although both species spent between 9 and 10 hours per day sleeping, the mainland sloths showed a preference for sleeping at night, whereas island sloths showed no preference for sleeping during the day or night. EEG activity during NREM sleep showed lower low-frequency power, and increased spindle and higher frequency power in island sloths when compared to mainland sloths. Conclusions: In sloths sleeping in the wild, predation pressure influenced the timing of sleep, but not the amount of time spent asleep. The preference for sleeping at night in mainland sloths may be a strategy to avoid detection by nocturnal cats. The pronounced differences in the NREM sleep EEG spectrum remain unexplained, but might be related to genetic or environmental factors.

Neoadjuvant chemoradiotherapy with or without panitumumab in patients with wild-type KRAS, locally advanced rectal cancer (LARC): a randomized, multicenter, phase II trial SAKK 41/07.

BACKGROUND: We conducted a randomized, phase II, multicenter study to evaluate the anti-epidermal growth factor receptor (EGFR) mAb panitumumab (P) in combination with chemoradiotherapy (CRT) with standard-dose capecitabine as neoadjuvant treatment for wild-type KRAS locally advanced rectal cancer (LARC). PATIENTS AND METHODS: Patients with wild-type KRAS, T3-4 and/or N+ LARC were randomly assigned to receive CRT with or without P (6 mg/kg). The primary end-point was pathological near-complete or complete tumor response (pNC/CR), defined as grade 3 (pNCR) or 4 (pCR) histological regression by Dworak classification (DC). RESULTS: Forty of 68 patients were randomly assigned to P + CRT and 28 to CRT. pNC/CR was achieved in 21 patients (53%) treated with P + CRT [95% confidence interval (CI) 36%-69%] versus 9 patients (32%) treated with CRT alone (95% CI: 16%-52%). pCR was achieved in 4 (10%) and 5 (18%) patients, and pNCR in 17 (43%) and 4 (14%) patients. In immunohistochemical analysis, most DC 3 cells were not apoptotic. The most common grade ≥3 toxic effects in the P + CRT/CRT arm were diarrhea (10%/6%) and anastomotic leakage (15%/4%). CONCLUSIONS: The addition of panitumumab to neoadjuvant CRT in patients with KRAS wild-type LARC resulted in a high pNC/CR rate, mostly grade 3 DC. The results of both treatment arms exceeded prespecified thresholds. The addition of panitumumab increased toxicity.

Immunolocalization of glyoxysomal malate synthase from soybean cotyledons (Glycine max. L.)

Malate synthase (MS; EC 4.1.3.2), an enzyme specific to the glyoxylate cycle, was studied in cotyledons of dark-grown soybean (Glycine max L) seedlings with light and electron microscopy techniques. Immunogold localization confirmed biochemical evidence that MS from soybean is a glyoxysomal matrix enzyme.