Selective impacts of subsistence hunting on mammal communities in Manu National Park, Peru

Research on impacts of subsistence hunting on habitat use and species communities of forest wildlife is limited. Subsistence hunting of mammals in one of the world’s most biodiverse region, Manu National Park, Peru, is considered sustainable but this is based on sparse evidence. We analysed change in species relative abundance and functional composition of mammal communities, including non-hunted species along a hunting pressure gradient. We used camera trap data and tested for confounding effects of environmental and disturbance gradients (distances to rivers, lakes, settlements, and trails; NDVI at survey point). We found that sites with no hunting or at further distances from settlements harbour relatively more species with a larger body mass, long generation lengths and small litters (primarily carnivores: 36% at non-hunted site vs 13-29% at hunted sites), indicating selective impacts of hunting pressure on mammal communities. However, all carnivore species still occurred at all sites. Species with a smaller body mass, short generation lengths, and large litters were more prevalent at the hunted sites (mostly rodents: 23 – 31% at hunted sites vs 20% at non-hunted site). Surprisingly, large herbivores appeared unaffected by hunting despite being one of the most hunted mammals in Manu (25% at non-hunted site vs 23-27% at hunted sites). Our findings suggest that current hunting pressure is largely sustainable with only local depletion of a few sensitive species. Habitat is more important for some species than hunting pressure (e.g. distance to lake), further emphasizing the importance of local forest management

Search algorithms as a framework for the optimization of drug combinations

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms, originally developed for digital communication, modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs with only one third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6-9 interventions in 80-90% of tests, compared with 15-30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution.Comment: 36 pages, 10 figures, revised versio

Fibrinogen storage disease without hypofibrinogenemia associated with estrogen therapy

BACKGROUND: Cytoplasmic inclusion bodies within hepatocytes may have different etiologies, including the Endoplasmic Reticulum Storage Diseases (ERSDs). ERSD is a pathological condition characterized by abnormal accumulation of proteins destined for secretion in the endoplasmic reticulum of hepatocytes; it may be congenital (primary) or acquired (secondary). Fibrinogen storage disease is a form of ERSD. CASE PRESENTATION: We present a case of fibrinogen storage disease secondary to estrogen replacement therapy. Its causal relationship to the drug is shown by histological, immunohistochemical and ultrastructural studies of paired liver biopsies obtained during and after the drug therapy. CONCLUSION: The liver biopsies of patients with idiopathic liver enzyme abnormalities should be carefully evaluated for cytoplasmic inclusion bodies and, although rare, fibrinogen deposits

Synthesis and characterisation of alpha-carboxynitrobenzyl photocaged l-aspartates for applications in time-resolved structural biology

We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged ⌊-aspartates for application in time-resolved structural biology. The resulting compounds were characterised in terms of UV/Vis absorption properties, aqueous solubility and stability, and photocleavage rates (τ = μs to ms) and quantum yields (φ = 0.05 to 0.14)

Non-Invasive Detection of a Small Number of Bioluminescent Cancer Cells In Vivo

Early detection of tumors can significantly improve the outcome of tumor treatment. One of the most frequently asked questions in cancer imaging is how many cells can be detected non-invasively in a live animal. Although many factors limit such detection, increasing the light emission from cells is one of the most effective ways of overcoming these limitations. Here, we describe development and utilization of a lentiviral vector containing enhanced firefly luciferase (luc2) gene. The resulting single cell clones of the mouse mammary gland tumor (4T1-luc2) showed stable light emission in the range of 10,000 photons/sec/cell. In some cases individual 4T1-luc2 cells inserted under the skin of a nu/nu mouse could be detected non-invasively using a cooled CCD camera in some cases. In addition, we showed that only few cells are needed to develop tumors in these mice and tumor progression can be monitored right after the cells are implanted. Significantly higher luciferase activity in these cells allowed us to detect micrometastases in both, syngeneic Balb/c and nu/nu mice

Restriction Site Extension PCR: A Novel Method for High-Throughput Characterization of Tagged DNA Fragments and Genome Walking

BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR) to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI) restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR), touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon) sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well

Endosialin expression in relation to clinicopathological and biological variables in rectal cancers with a Swedish clinical trial of preoperative radiotherapy

<p>Abstract</p> <p>Background</p> <p>The importance of changes in tumour-associated stroma for tumour initiation and progression has been established. Endosialin is expressed in fibroblasts and pericytes of blood vessels in several types of tumours, and is involved in the progression of colorectal cancer. In order to see whether endosialin was related to radiotherapy (RT) response, and clinicopathological and biological variables, we investigated endosialin expression in rectal cancers from the patients who participated in a Swedish clinical trial of preoperative RT.</p> <p>Methods</p> <p>Endosialin was immunohistochemically examined in normal mucosa, including distant (<it>n </it>= 72) and adjacent (<it>n </it>= 112) normal mucosa, and primary tumours (<it>n </it>= 135). Seventy-three of 135 patients received surgery alone and 62 received additional preoperative RT.</p> <p>Results</p> <p>Endosialin expression in the stroma increased from normal mucosa to tumour (<it>p </it>< 0.0001) both in RT and non-RT group. In the RT group, endosialin expression in the stroma was positively associated with expression of cyclooxygenase-2 (Cox-2) (<it>p </it>= 0.03), p73 (<it>p </it>= 0.01) and phosphates of regenerating liver (PRL) (<it>p </it>= 0.002). Endosialin expression in the tumour cells of both in the RT group (<it>p </it>= 0.01) and the non-RT group (<it>p </it>= 0.06) was observed more often in tumours with an infiltrative growth pattern than in tumours with an expansive growth pattern. In the RT group, endosialin expression in tumour cells was positively related to PRL expression (<it>p </it>= 0.02), whereas in the non-RT group, endosialin expression in tumour cells was positively related to p73 expression (<it>p </it>= 0.01).</p> <p>Conclusions</p> <p>Endosialin expression may be involved in the progression of rectal cancers, and was related to Cox-2, p73 and PRL expression. However, a direct relationship between endosialin expression and RT responses in patients was not found.</p

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Non-destructive detection of cross-sectional strain and defect structure in an individual Ag five-fold twinned nanowire by 3D electron diffraction mapping

Coherent x-ray diffraction investigations on Ag five-fold twinned nanowires (FTNWs) have drawn controversial conclusions concerning whether the intrinsic 7.35° angular gap could be compensated homogeneously through phase transformation or inhomogeneously by forming disclination strain field. In those studies, the x-ray techniques only provided an ensemble average of the structural information from all the Ag nanowires. Here, using three-dimensional (3D) electron diffraction mapping approach, we non-destructively explore the cross-sectional strain and the related strain-relief defect structures of an individual Ag FTNW with diameter about 30 nm. The quantitative analysis of the fine structure of intensity distribution combining with kinematic electron diffraction simulation confirms that for such a Ag FTNW, the intrinsic 7.35° angular deficiency results in an inhomogeneous strain field within each single crystalline segment consistent with the disclination model of stress-relief. Moreover, the five crystalline segments are found to be strained differently. Modeling analysis in combination with system energy calculation further indicates that the elastic strain energy within some crystalline segments, could be partially relieved by the creation of stacking fault layers near the twin boundaries. Our study demonstrates that 3D electron diffraction mapping is a powerful tool for the cross-sectional strain analysis of complex 1D nanostructures