bluuebunny/crossref_metadata_2025 huggingface dataset:
Wind‐formed gravel bed forms, Wright Valley, Antarctica
Authors: Gillies John A. , Nickling William G. , Tilson Michael , Furtak‐Cole Eden
Published: September 2012

Bed forms composed of gravel size particles (≈50% of particles >4 mm) are observed in the Wright Valley of the McMurdo Dry Valley system in Antarctica. These bed forms are characterized by a very asymmetrical shape with a mean aspect ratio of 0.025 (standard deviation 0.005), mean wavelength of 2.7 m (±0.49 m), and a mean height of 0.06 m (±0.01 m). Particle size analysis of the bed form sediments shows bimodality with a peak near 9 mm and another between 0.5 mm and 0.25 mm. Time‐integrated sediment trap samples of horizontal saltation and creep flux indicate the flux of particles ≥4 mm during the two‐year monitoring period was extremely low. Measurements of the horizontal displacement of tracer particles (14 mm, 12 mm, 10 mm, 8 mm, and 6 mm diameter) placed onto the bed forms corroborate the low particle flux measurements and limited movement of particles. The bed forms share form and grain size characteristics with both ripples and mega‐ripples, showing poor sorting of particles across a single wavelength except for a slight coarsening at the crest similar to ripples, but their sinuosity suggest that transverse instabilities affect their formation similar to mega‐ripples. Based on the data for the prevailing environmental conditions it can be argued that the Wright Valley form is an expression of gravel particles moved solely by highly intermittent creep processes. This also argues for the need for a very long period of time for their evolution, on the order of centuries.
The 2005 volcano‐tectonic earthquake swarm in the Andaman Sea: Triggered by the 2004 great Sumatra‐Andaman earthquake
Authors: Kundu Bhaskar , Legrand Denis , Gahalaut Kalpna , Gahalaut Vineet K. , Mahesh P. , Kamesh Raju K. A. , Catherine J. K. , Ambikapthy A. , Chadha R. K.
Published: September 2012

A 6 day duration earthquakes swarm occurred in the Andaman Sea, 31 days after the giant 2004 Sumatra‐Andaman earthquake (Mw 9.2). The swarm occurred less than 100 km from the eastern edge of the 2004 earthquake rupture and is the most energetic ever recorded in the world. The earthquakes swarm appear to have occurred on en echelon fault system bounded by the two main right‐lateral strike‐slip faults, namely, the Seulimeum Strand of Sumatra Fault system (SEU) and the West Andaman Fault (WAF). At the beginning of the swarm, earthquakes with predominantly strike‐slip focal mechanisms occurred which were followed by earthquakes with predominantly normal faulting focal mechanisms having significant deviatoric component. Highbvalue, presence of double slope in the Gutenberg‐Richter relation, presence of monogenetic submarine volcanoes in the region of the swarm and the earthquake focal mechanisms suggest that the swarm was of volcano‐tectonic origin and fluid flow played an important role in its occurrence. Indeed, our modeling suggests that it was triggered by the 2004 Sumatra‐Andaman earthquake through poroelastic relaxation of the coseismic stresses.
Multiple flow solutions in buoyancy induced convection in a porous square box
Authors: Henry D. , Touihri R. , Bouhlila R. , Ben Hadid H.
Published: September 2012

The convection induced by buoyancy effects in a porous square cavity has been investigated numerically using a spectral element code with bifurcation tools. The complex bifurcation diagram initiated from the first six primary bifurcation points corresponding to the onset of convection from the trivial no‐flow solution has been calculated. Four branches of stable steady solutions have been found, corresponding to one‐roll, two‐roll, three‐roll and four‐roll flow structures. The domain of existence of these stable solutions, i.e., the Rayleigh number (Ra) range in which such solutions can potentially be observed, has been precisely determined. It is shown that there exist Ra ranges where different flow solutions can be stable together. The stable branches all terminate at Hopf bifurcation points beyond which oscillatory solutions have been computed.
Hydraulic resistance to overland flow on surfaces with partially submerged vegetation
Authors: Kim Jongho , Ivanov Valeriy Y. , Katopodes Nikolaos D.
Published: September 2012

This study investigates numerically the characteristics of upscaling the Manning resistance coefficient (nt) for areas covered by partially submerged vegetation elements, such as shrub or tree stems. A number of high‐resolution hydrodynamic simulations were carried out corresponding to scenarios with different domain slopes (S), inflow rates (Q), bed roughness (nb), and vegetation cover fractions (Vf). Using simulations performed at fine space‐time scales, two methods were developed for computing the upscaled Manning coefficient, termed “Equivalent Roughness Surface (ERS)” and “Equivalent Friction Slope (EFS).” Results obtained with these two methods indicate that both yield highly correlated estimates of nt. The effects of four independent variables (Vf, S, Q, and nb) on nt were further investigated. First, as Vf increases, nt also grows. Second, two distinct modes of the relationship between S and nt for a fixed Vf and Q emerge: a positive dependence at low‐flow rates and a negative dependence at high‐flow rates. For a fixed Vf and S, two distinct modes of the relationship between Q and nt are also identified: a positive dependence at mild domain slopes and a negative dependence at steep slopes. A regression analysis shows that the two conflicting trends can occur depending on whether the variability of flow depth with respect to S (or Q) is greater than the ratio of h and S (or Q). Third, a rougher soil bed (i.e., larger values of nb) implies a higher resistance due to vegetation. Last, the study argues that nt increases as h increases and decreases as V increases. A generic regression relation that includes all four of the above variables and the difference nt − nb (i.e., the additional resistance due to partially submerged vegetation representing the sum of the form and wave resistances) was developed. The range of applicability of this relation is given by the following conditions: Vf ≤ 0.5, 0.1 ≤ S ≤ 1.1, and 0.0001 ≤ Q ≤ 0.01. The difference nt − nb computed from the developed regression relation was compared with estimates reported by five different studies. Furthermore, the simulated wave resistance coefficients were compared with those predicted from an equation in a previous study; the estimates were consistent in the range of experimental conditions for which the latter equation was developed. The relationship is sufficiently general and applicable to other flow conditions with partially submerged roughness elements.
Characterization of residence time variability in a managed monomictic reservoir
Authors: Andradóttir H. Ó. , Rueda F. J. , Armengol J. , Marcé R.
Published: September 2012

The average length of time land‐borne compounds remain within an aquatic system is one of the key parameters controlling its biochemical processes. This study explores the magnitude and sources of daily, seasonal, and interannual variability of river water residence time in the Sau Reservoir, a prototypical example of a Mediterranean water supply. Daily estimates of residence time from 1998 to 2005 were obtained from a series of tracer experiments simulated with a one‐dimensional physical model, based on actual observations and synthetic scenarios. Results highlight that multiple in situ factors, both natural and managed by humans, affect the residence time in reservoirs. Simulated residence times varied on average ∼30% on a daily basis, as a result of natural meteorological (17%) and river inflow temperature (11%) variability. The management of withdrawal depths largely controlled the seasonal variations: The practice of withdrawing water from the shallowest outlet, which was close to the intrusion level of summer inflows, promoted shorter residence times in summers than winters. Interannual variability was primarily associated with the natural variability of inflow volume (25%), and secondarily with surface meteorology (8%). Excessive withdrawals prior to and during long dry periods, however, drastically reduced the reservoir storage capacity and withdrawal options, leading to shorter residence times in dry years. The flushing time, calculated as the ratio of storage volume and flow rates, captured the trends in annual mean residence times reasonably well but not daily and seasonal residence times.
Direct geoelectrical evidence of mass transfer at the laboratory scale
Authors: Swanson Ryan D. , Singha Kamini , Day‐Lewis Frederick D. , Binley Andrew , Keating Kristina , Haggerty Roy
Published: September 2012

Previous field‐scale experimental data and numerical modeling suggest that the dual‐domain mass transfer (DDMT) of electrolytic tracers has an observable geoelectrical signature. Here we present controlled laboratory experiments confirming the electrical signature of DDMT and demonstrate the use of time‐lapse electrical measurements in conjunction with concentration measurements to estimate the parameters controlling DDMT, i.e., the mobile and immobile porosity and rate at which solute exchanges between mobile and immobile domains. We conducted column tracer tests on unconsolidated quartz sand and a material with a high secondary porosity: the zeolite clinoptilolite. During NaCl tracer tests we collected nearly colocated bulk direct‐current electrical conductivity (σb) and fluid conductivity (σf) measurements. Our results for the zeolite show (1) extensive tailing and (2) a hysteretic relation betweenσfandσb, thus providing evidence of mass transfer not observed within the quartz sand. To identify best‐fit parameters and evaluate parameter sensitivity, we performed over 2700 simulations ofσf, varying the immobile and mobile domain and mass transfer rate. We emphasized the fit to late‐time tailing by minimizing the Box‐Cox power transformed root‐mean square error between the observed and simulatedσf. Low‐field proton nuclear magnetic resonance (NMR) measurements provide an independent quantification of the volumes of the mobile and immobile domains. The best‐fit parameters based onσfmatch the NMR measurements of the immobile and mobile domain porosities and provide the first direct electrical evidence for DDMT. Our results underscore the potential of using electrical measurements for DDMT parameter inference.
ADAM28 is elevated in humans with the metabolic syndrome and is a novel sheddase of human tumour necrosis factor‐α
Authors: Jowett Jeremy B M , Okada Yasunori , Leedman Peter J , Curran Joanne E , Johnson Matthew P , Moses Eric K , Goring Harald H H , Mochizuki Satsuki , Blangero John , Stone Leah , Allen Holly , Mitchell Chris , Matthews Vance B
Published: September 2012

Metalloproteinases are implicated in cleaving numerous proinflammatory mediators from the cell surface. Interestingly, the elevated levels of tumour necrosis factor‐α (TNF‐α) have been associated with the metabolic syndrome. We aimed to ascertain whether the human metalloproteinase ADAM28 correlates with parameters of the metabolic syndrome and whether ADAM28 is a novel sheddase of human TNF‐α. To identify novel metalloproteinases associated with the metabolic syndrome, we conducted microarray studies on peripheral blood mononuclear cells from a well characterised human cohort. Human ADAM28 and TNF‐α were overexpressed and ADAM28 expression or activity was reduced with small‐interfering RNA (siRNA) or pharmacological inhibition. TNF‐α levels were measured in cell supernatant by enzyme‐linked immunosorbent assay. We also conducted ADAM28 inhibition studies in human THP‐1 macrophages. Human ADAM28 expression levels were positively correlated with parameters of the metabolic syndrome. When human ADAM28 and TNF‐α were overexpressed in HEK293 cells, both proteins co‐localised, co‐immunoprecipitated and promoted TNF‐α shedding. The shedding was significantly reduced when ADAM28 activity was inhibited or ADAM28 expression was downregulated. In human THP‐1 macrophages, endogenous ADAM28 and TNF‐α were co‐expressed and TNF‐α shedding was significantly reduced when ADAM28 was inhibited by pharmacological inhibition or siRNA knockdown. Our data suggest a novel mechanistic role for the metalloproteinase ADAM28 in inflammation, obesity and type 2 diabetes.
Modulation of CD147-induced matrix metalloproteinase activity: role of CD147 N-glycosylation
Authors: Huang Wan , Luo Wen-Juan , Zhu Ping , Tang Juan , Yu Xiao-Ling , Cui Hong-Yong , Wang Bin , Zhang Yang , Jiang Jian-Li , Chen Zhi-Nan
Published: September 2012

Degradation of the basement membrane by MMPs (matrix metalloproteinases) is one of the most critical steps in tumour progression. CD147 is a tumour-associated antigen that plays a key regulatory role for MMP activities. In the present study, mass spectrum analysis demonstrated that the purified native CD147 from human lung cancer tissue was N-glycosylated and contained a series of high-mannose and complex-type N-linked glycan structures. Moreover, native glycosylated CD147 existed exclusively as oligomers in solution and directly stimulated MMP production more efficiently than non-glycosylated prokaryotic CD147. The glycosylation site mutation results indicated that, among three N-glycan attachment sites, the N152Q mutants were retained in the endoplasmic reticulum and unfolded protein response signalling was activated. This improper intracellular accumulation impaired its MMP-inducing activity. Increased β1,6-branching of N-glycans as a result of overexpression of GnT-V (N-acetylglucosaminyltransferase V) plays an important role in tumour metastasis. In the present study, we identified CD147 as a target protein of GnT-V and found that overexpression of GnT-V resulted in an elevated level of CD147 at the plasma membrane and in cell-conditioned medium, thereby increasing the induction of MMPs. The present study reveals the important role of N-glycosylation of CD147 in its biological function and implied that targeting aberrant β1,6-branching of N-glycans on CD147 would be valuable for the development of novel therapeutic modalities against carcinoma.
Protein kinase Cβ is critical for the metabolic switch to glycolysis following B-cell antigen receptor engagement
Authors: Blair Derek , Dufort Fay J. , Chiles Thomas C.
Published: September 2012

Signals derived from the BCR (B-cell antigen receptor) control survival, development and antigenic responses. One mechanism by which BCR signals may mediate these responses is by regulating cell metabolism. Indeed, the bioenergetic demands of naïve B-cells increase following BCR engagement and are characterized by a metabolic switch to aerobic glycolysis; however, the signalling pathways involved in this metabolic reprogramming are poorly defined. The PKC (protein kinase C) family plays an integral role in B-cell survival and antigenic responses. Using pharmacological inhibition and mice deficient in PKCβ, we demonstrate an essential role of PKCβ in BCR-induced glycolysis in B-cells. In contrast, mice deficient in PKCδ exhibit glycolytic rates comparable with those of wild-type B-cells following BCR cross-linking. The induction of several glycolytic genes following BCR engagement is impaired in PKCβ-deficient B-cells. Moreover, blocking glycolysis results in decreased survival of B-cells despite BCR engagement. The results establish a definitive role for PKCβ in the metabolic switch to glycolysis following BCR engagement of naïve B-cells.
A versatile proline/alanine transporter in the unicellular pathogen Leishmania donovani regulates amino acid homoeostasis and osmotic stress responses
Authors: Inbar Ehud , Schlisselberg Doreen , Suter Grotemeyer Marianne , Rentsch Doris , Zilberstein Dan
Published: September 2012

Unlike all other organisms, parasitic protozoa of the family Trypanosomatidae maintain a large cellular pool of proline that, together with the alanine pool, serve as alternative carbon sources as well as reservoirs of organic osmolytes. These reflect adaptation to their insect vectors whose haemolymphs are exceptionally rich in the two amino acids. In the present study we identify and characterize a new neutral amino acid transporter, LdAAP24, that translocates proline and alanine across the Leishmania donovani plasma membrane. This transporter fulfils multiple functions: it is the sole supplier for the intracellular pool of proline and contributes to the alanine pool; it is essential for cell volume regulation after osmotic stress; and it regulates the transport and homoeostasis of glutamate and arginine, none of which are its substrates. Notably, we provide evidence that proline and alanine exhibit different roles in the parasitic response to hypotonic shock; alanine affects swelling, whereas proline influences the rate of volume recovery. On the basis of our data we suggest that LdAAP24 plays a key role in parasite adaptation to its varying environments in host and vector, a phenomenon essential for successful parasitism.
Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5
Authors: Senisterra Guillermo , Wu Hong , Allali-Hassani Abdellah , Wasney Gregory A. , Barsyte-Lovejoy Dalia , Dombrovski Ludmila , Dong Aiping , Nguyen Kong T. , Smil David , Bolshan Yuri , Hajian Taraneh , He Hao , Seitova Alma , Chau Irene , Li Fengling , Poda Gennadiy , Couture Jean-François , Brown Peter J. , Al-Awar Rima , Schapira Matthieu , Arrowsmith Cheryl H. , Vedadi Masoud
Published: September 2012

WDR5 (WD40 repeat protein 5) is an essential component of the human trithorax-like family of SET1 [Su(var)3–9 enhancer-of-zeste trithorax 1] methyltransferase complexes that carry out trimethylation of histone 3 Lys4 (H3K4me3), play key roles in development and are abnormally expressed in many cancers. In the present study, we show that the interaction between WDR5 and peptides from the catalytic domain of MLL (mixed-lineage leukaemia protein) (KMT2) can be antagonized with a small molecule. Structural and biophysical analysis show that this antagonist binds in the WDR5 peptide-binding pocket with a Kd of 450 nM and inhibits the catalytic activity of the MLL core complex in vitro. The degree of inhibition was enhanced at lower protein concentrations consistent with a role for WDR5 in directly stabilizing the MLL multiprotein complex. Our data demonstrate inhibition of an important protein–protein interaction and form the basis for further development of inhibitors of WDR5-dependent enzymes implicated in MLL-rearranged leukaemias or other cancers.
Platelet‐rich plasma‐derived growth factors promote osteogenic differentiation of rat muscle satellite cells: in vitro and in vivo studies
Authors: Huang Shengyun , Wang Zuolin
Published: September 2012

PRP (platelet‐rich plasma)‐derived growth factors are a new application of tissue engineering and a developing area for researchers and clinicians. We have assessed the effects of PRP‐derived growth factors on the proliferation and osteogenic differentiation of rMSCs (rat muscle satellite cells), and constructed a novel tissue engineering bone composed of PRP‐derived growth factors and rMSCs. PRP were created by a freeze‐thaw process. rMSCs were isolated from rat masticatory muscle using serial platings technique. Wst‐1 assay, SEM (scanning electron microscopy), ALP (alkaline phosphatase) activity, total protein concentration, AR (Alizarin red S) staining, calcium analyses and RT‐PCR (reverse transcription–PCR) of osteogenic‐related genes were used to assess the effect of PRP‐derived growth factors on proliferation and osteogenic differentiation of cultured rMSCs on scaffolds. The different composite scaffolds were implanted to the subcutaneous spaces of nude mice. H&E (haematoxylin and eosin) and Masson's trichrome staining were used to examine the ectopic bone formation. In vitro, we found that PRP‐derived growth factors showed excellent cell compatibility and significantly enhanced cell proliferation over serum and control groups at 48 and 72 h. SEM, ALP activity, AR staining, calcium analyses and RT‐PCR showed that PRP‐derived growth factors significantly increased cells osteogenic differentiation when compared with other groups. In vivo examination showed that more fibrous tissue capsule and bone with lamellar structures appeared in PRP‐derived growth factors groups. These results suggest that the PRP‐derived growth factors significantly promote rMSCs proliferation, osteogenic differentiation compared with serum and scaffolds alone, and may be suitable for stem cell growth factors delivery and bone tissue engineering.
BMP4 can generate primordial germ cells from bone‐marrow‐derived pluripotent stem cells
Authors: Shirazi Reza , Zarnani Amir Hassan , Soleimani Masoud , Abdolvahabi Mir Abbas , Nayernia Karim , Kashani Iraj Ragerdi
Published: September 2012

Evidence of germ cell derivation from embryonic and somatic stem cells provides an in vitro model for the study of germ cell development, associated epigenetic modification and mammalian gametogenesis. More importantly, in vitro derived gametes also represent a potential strategy for treating infertility. In mammals, male and female gametes, oocyte and sperm, are derived from a specific cell population, PGCs (primordial germ cells) that segregate early in embryogenesis. We have isolated pluripotent SSEA‐1+ (stage‐specific embryonic antigen‐1+) cells from mice bone marrow using a MACS (magnetic‐activated cell sorting) system. SSEA‐1+ cells were directly separated from the suspension of MMCs (murine mononuclear cells) harvested from bone marrow of 2–4‐week‐old mice. Flow‐cytometry assay immediately after sorting and culturing under undifferentiated condition showed 55±7% and 87±4% purity respectively. RT‐PCR (reverse transcription–PCR) analysis after differentiation of SSEA‐1+ cells into derivations of three germ layers showed the pluripotency properties of isolated cells. SSEA‐1+ cells were induced to differentiate along germ cell lineage by adding BMP4 (bone morphogenic factor‐4) to the medium. Regarding the expression of germ cell markers (PGCs, male and female germ cell lineage), it was found that adding exogenous BMP4 to culture medium could differentiate pluripotent SSEA‐1+ cells isolated from an adult tissue into gamete precursors, PGCs. Differentiated cells expressed specific molecular markers of PGCs, including Oct4, fragilis, Stella and Mvh (mouse vasa homologue). Therefore BMP4 is insufficient to induce SSEA‐1+ cells derived from PGCs to develop further into late germ cells in vitro.
Cardiomyocyte apoptosis in ischaemia‐reperfusion due to the exogenous oxidants at the time of reperfusion
Authors: Rosca Ana‐Maria , Matei Camelia , Dragan Emanuel , Burlacu Alexandrina
Published: September 2012

Various studies performed on different models have demonstrated that apoptosis occurs in ischaemic‐reperfused myocardium in vivo; however, the individual contribution of ischaemia and reperfusion to CMC (cardiomyocyte) apoptosis remains uncertain. We have determined the main inducer of CMC apoptosis in ischaemia‐reperfusion by exposing CMCs to either 30 min ischaemia followed by reperfusion or to 25‐OH‐cholesterol (25‐hydroxycholesterol) for 1–3 days. Both ischaemia‐reperfusion and exogenous oxidants increased the Bax/Bcl‐2 ratio, a favourable effect for the apoptotic process. However, apoptosis was not observed in ischaemic CMCs in the absence of reperfusion. Moreover, reperfusion after 30 min ischaemia did not make an important contribution to CMC apoptosis in culture in terms of caspase 3 activation. In contrast, 25‐OH‐cholesterol promoted CMC apoptosis by a caspase 3‐dependent mechanism that involved the transcriptional activation of the pro‐apoptotic protein, Bax and post‐translational degradation of the anti‐apoptotic protein, Bcl‐2. From these results, we conclude that CMC apoptosis is not induced by ischaemia per se, but by the oxidants from the surrounding environment at the time of reperfusion. These exogenous oxidants exacerbate the alterations induced by ischaemia and complete the apoptotic process at the time when ATP and glucose levels are restored.
Hypericin‐PDT‐induced rapid necrotic death in human squamous cell carcinoma cultures after multiple treatment
Authors: Sharma Krishna V. , Davids Lester M.
Published: September 2012

PDT (photodynamic therapy) has been used for the treatment of NMCC (non‐melanoma cutaneous cancer) particularly, human SCC (squamous cell carcinoma). However, the nature of the photosensitizer, the activation light source and the mode of cell death induced post‐PDT remains elusive. We tried to optimize PDT using the light‐activated (320–400 nm) St John's Wort‐derived compound, Hyp (hypericin). The work highlights the potential mode of cell death and the increased efficacy of the technique associated with multiple Hyp‐PDT treatment. SCC cells were exposed to different concentrations of Hyp and activated with light at 1 J/cm2 for 1 or 2 days. Thereafter with the optimum dose of Hyp proliferation, ROS (reactive oxygen species), and apoptosis were analysed by XTT [2,3‐bis‐(2‐methoxy‐4‐nitro‐5‐sulfophenyl)‐2H‐tetrazolium‐5‐carboxanilide] assay, FACS analysis and Fluorescent/Phase contrast microscopy was carried out for morphological studies. Hyp‐PDT produces more ROS after 1 day compared with 2 days and the mode of cell death is a necrotic caspase‐independent mechanism. We propose a novel ‘double‐hit/2‐day’ strategy to reduce the viability in SCC using Hyp‐based PDT as an adjunctive treatment modality.
Phenotyping for drought tolerance in grain crops: when is it useful to breeders?
Authors: Passioura J. B.
Published: September 2012

Breeding for drought tolerance in grain crops is not a generic issue. Periods of drought vary in length, timing and intensity and different traits are important with different types of drought. The search for generic drought tolerance using single-gene transformations has been disappointing. It has typically concentrated on survival of plants suffering from severe water stress, which is rarely an important trait in crops. More promising approaches that target complex traits tailored to specific requirements at the different main stages of the life of a crop, during: establishment, vegetative development, floral development and grain growth are outlined. The challenge is to devise inexpensive and effective ways of identifying promising phenotypes with the aim of aligning them with genomic information to identify molecular markers useful to breeders. Controlled environments offer the stability to search for attractive phenotypes or genotypes in a specific type of drought. The recent availability of robots for measuring large number of plants means that large numbers of genotypes can be readily phenotyped. However, controlled environments differ greatly from those in the field. Devising pot experiments that cater for important yield-determining processes in the field is difficult, especially when water is limiting. Thus, breeders are unlikely to take much notice of research in controlled environments unless the worth of specific traits has been demonstrated in the field. An essential link in translating laboratory research to the field is the development of novel genotypes that incorporate gene(s) expressing a promising trait into breeding lines that are adapted to target field environments. Only if the novel genotypes perform well in the field are they likely to gain the interest of breeders. High throughput phenotyping will play a pivotal role in this process.
Effects of different manure application rates on soil properties, nutrient use, and crop yield during dryland maize farming
Authors: Hou Xianqing , Wang Xiaojuan , Li Rong , Jia Zhikuan , Liang Lianyou , Wang Junpeng , Nie Junfeng , Chen Xin , Wang Zhen
Published: September 2012

The combined application of manure and chemical fertiliser has major effects on soil physico-chemical and biological properties, and it increases crop yields. A 4-year study was conducted to study the effects of the application of high (HM 22 500 kg/ha), medium (MM 15 000 kg/ha), and low (LM 7500 kg/ha) rates of manure in combination with conventional chemical fertiliser. We evaluated the effects on soil properties, nutrient use, and crop yield in a continuous-cropping maize system. We also compared the three manure treatments with chemical fertiliser-only (CF-only) and no fertiliser (NF) treatments during 2007–2010 in semi-arid conditions. Compared with CF-only and NF, manure combined with chemical fertiliser produced a lower soil bulk density and significantly increased the >0.25-mm water-stable aggregate content, which was higher with increasing manure application rates. The duration of increased soil enzyme activity after manure application depended on the manure application rate; HM produced a significantly higher increase in soil enzyme activity than CF-only and NF during 2007–2010. Manure combined with chemical fertiliser significantly increased crop yield and nitrogen (N) content of the crop organs, showing that this treatment enhanced the use of N fertiliser. Soil properties may be conserved by the MM treatment, which improved soil properties while increasing crop yield, because there was no significant difference in the residual level of N with the MM and CF-only treatments. Therefore, the MM treatment may be an appropriate soil fertiliser treatment for dryland maize farming.
Evaluation of soil physical quality of irrigated agroecosystems in a semi-arid region of North-eastern Brazil
Authors: Pereira V. P. , Ortiz-Escobar M. E. , Rocha G. C. , Junior R. N. Assis , Oliveira T. S.
Published: September 2012

Concern about soil physical quality has grown in recent years, particularly in view of serious problems caused by intensive soil use. We hypothesised that improper soil management in irrigated areas damages the structure of sensitive soils in some regions in North-eastern Brazil. The aim of the study was to evaluate the physical quality of irrigated soils planted with annual and perennial crops, compared with soils under natural vegetation in Ceará State, Brazil. Measurements were made of least limiting water range (LLWR), the S index, and relative density. Undisturbed soil samples were collected at two depths (5–10 and 20–25 cm) in four cultivated areas (banana, guava, pasture, and maize/bean in succession) and two natural vegetation areas (NV1, NV2) adjacent to the cultivated areas. All sites were in the Jaguaribe-Apodi Irrigated District, Limoeiro do Norte, Ceará, Brazil. The LLWR was determined using the water retention curve, soil resistance to penetration, and soil bulk density, which are parameters needed to obtain the upper and lower limits of LLWR. The S index was obtained from the water retention curve. The relative density was obtained from the relationship between bulk density and maximum density obtained from the Proctor test. The S index varied as a function of soil management. The variation in LLWR differed between the studied areas as a function of soil bulk density. The relative densities for NV1 and NV2 were lower than for cultivated areas, showing that intensive soil use has caused compaction. The studied parameters seem to be good indicators of soil physical quality, and it was noticed that soils under cultivation suffer an alteration of their structure relative to soils under natural vegetation.
Field validation of a free-agent cellular automata model of fire spread with fire - atmosphere coupling
Authors: Achtemeier Gary L.
Published: September 2012

A cellular automata fire model represents ‘elements’ of fire by autonomous agents. A few simple algebraic expressions substituted for complex physical and meteorological processes and solved iteratively yield simulations for ‘super-diffusive’ fire spread and coupled surface-layer (2-m) fire–atmosphere processes. Pressure anomalies, which are integrals of the thermal properties of the overlying heated plume, drive the surface winds around and through the fire. Five simulations with differing fuel and wind conditions were compared with fire and meteorological data from an experimental grassfire (FireFlux). The fire model accurately simulated bulk patterns of measured time-series of 2-m winds at two towers and observed fire behaviour (spread rate, flaming depth and heat released). Fidelity to spatial windfields in the vicinity of the fire was similar to results from full-physics fire models for other grassfires. Accurate predictions of fire spread depend critically on accurate wind speeds and directions at the location of the fire. Simulated fire–atmosphere coupling using FireFlux data increased wind speeds across the fire line by up to a factor of three. With its computational speed relative to full-physics models, the fire model can inform full-physics modellers regarding problems of interest. Although the fire model is tested for homogeneous fuels on flat terrain, the model is designed for simulating complex distributions of fire within heterogeneous distributions of fuels over complex landscapes.
Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end
Authors: Bai Hua , Kath James E. , Zörgiebel Felix Manuel , Sun Mingxuan , Ghosh Pallavi , Hatfull Graham F. , Grindley Nigel D. F. , Marko John F.
Published: September 2012

Enzyme rates are usually considered to be dependent on local properties of the molecules involved in reactions. However, for large molecules, distant constraints might affect reaction rates by affecting dynamics leading to transition states. In single-molecule experiments we have found that enzymes that relax DNA torsional stress display rates that depend strongly on how the distant ends of the molecule are constrained; experiments with different-sized particles tethered to the end of 10-kb DNAs reveal enzyme rates inversely correlated with particle drag coefficients. This effect can be understood in terms of the coupling between molecule extension and local molecular stresses: The rate of bead thermal motion controls the rate at which transition states are visited in the middle of a long DNA. Importantly, we have also observed this effect for reactions on unsupercoiled DNA; other enzymes show rates unaffected by bead size. Our results reveal a unique mechanism through which enzyme rates can be controlled by constraints on macromolecular or supramolecular substrates.
ORMDL3 is an inducible lung epithelial gene regulating metalloproteases, chemokines, OAS, and ATF6
Authors: Miller Marina , Tam Arvin B. , Cho Jae Youn , Doherty Taylor A. , Pham Alexa , Khorram Naseem , Rosenthal Peter , Mueller James L. , Hoffman Hal M. , Suzukawa Maho , Niwa Maho , Broide David H.
Published: September 2012

Orosomucoid like 3 (ORMDL3) has been strongly linked with asthma in genetic association studies, but its function in asthma is unknown. We demonstrate that in mice ORMDL3 is an allergen and cytokine (IL-4 or IL-13) inducible endoplasmic reticulum (ER) gene expressed predominantly in airway epithelial cells. Allergen challenge induces a 127-fold increase in ORMDL3 mRNA in bronchial epithelium in WT mice, with lesser 15-fold increases in ORMDL-2 and no changes in ORMDL-1. Studies of STAT-6–deficient mice demonstrated that ORMDL3 mRNA induction highly depends on STAT-6. Transfection of ORMDL3 in human bronchial epithelial cells in vitro induced expression of metalloproteases (MMP-9, ADAM-8), CC chemokines (CCL-20), CXC chemokines (IL-8, CXCL-10, CXCL-11), oligoadenylate synthetases (OAS) genes, and selectively activated activating transcription factor 6 (ATF6), an unfolded protein response (UPR) pathway transcription factor. siRNA knockdown of ATF-6α in lung epithelial cells inhibited expression of SERCA2b, which has been implicated in airway remodeling in asthma. In addition, transfection of ORMDL3 in lung epithelial cells activated ATF6α and induced SERCA2b. These studies provide evidence of the inducible nature of ORMDL3 ER expression in particular in bronchial epithelial cells and suggest an ER UPR pathway through which ORMDL3 may be linked to asthma.
TCR signaling via Tec kinase ITK and interferon regulatory factor 4 (IRF4) regulates CD8
+
T-cell differentiation
Authors: Nayar Ribhu , Enos Megan , Prince Amanda , Shin HyunMu , Hemmers Saskia , Jiang Jian-kang , Klein Ulf , Thomas Craig J. , Berg Leslie J.
Published: September 2012

CD8
+
T-cell development in the thymus generates a predominant population of conventional naive cells, along with minor populations of “innate” T cells that resemble memory cells. Recent studies analyzing a variety of KO or knock-in mice have indicated that impairments in the T-cell receptor (TCR) signaling pathway produce increased numbers of innate CD8
+
T cells, characterized by their high expression of CD44, CD122, CXCR3, and the transcription factor, Eomesodermin (Eomes). One component of this altered development is a non-CD8
+
T cell-intrinsic role for IL-4. To determine whether reduced TCR signaling within the CD8
+
T cells might also contribute to this pathway, we investigated the role of the transcription factor, IFN regulatory factor 4 (IRF4). IRF4 is up-regulated following TCR stimulation in WT T cells; further, this up-regulation is impaired in T cells treated with a small-molecule inhibitor of the Tec family tyrosine kinase, IL-2 inducible T-cell kinase (ITK). In contrast to WT cells, activation of IRF4-deficient CD8
+
T cells leads to rapid and robust expression of Eomes, which is further enhanced by IL-4 stimulation. In addition, inhibition of ITK together with IL-4 increases Eomeso up-regulation. These data indicate that ITK signaling promotes IRF4 up-regulation following CD8
+
T-cell activation and that this signaling pathway normally suppresses Eomes expression, thereby regulating the differentiation pathway of CD8
+
T cells.
Canonical Wnt signaling regulates Slug activity and links epithelial–mesenchymal transition with epigenetic Breast Cancer 1, Early Onset (BRCA1) repression
Authors: Wu Zhao-Qiu , Li Xiao-Yan , Hu Casey Yuexian , Ford Michael , Kleer Celina G. , Weiss Stephen J.
Published: September 2012

Slug (Snail2) plays critical roles in regulating the epithelial–mesenchymal transition (EMT) programs operative during development and disease. However, the means by which Slug activity is controlled remain unclear. Herein we identify an unrecognized canonical Wnt/GSK3β/β-Trcp1 axis that controls Slug activity. In the absence of Wnt signaling, Slug is phosphorylated by GSK3β and subsequently undergoes β-Trcp1–dependent ubiquitination and proteosomal degradation. Alternatively, in the presence of canonical Wnt ligands, GSK3β kinase activity is inhibited, nuclear Slug levels increase, and EMT programs are initiated. Consistent with recent studies describing correlative associations in basal-like breast cancers between Wnt signaling, increased Slug levels, and reduced expression of the tumor suppressor Breast Cancer 1, Early Onset (BRCA1), further studies demonstrate that Slug—as well as Snail—directly represses BRCA1 expression by recruiting the chromatin-demethylase, LSD1, and binding to a series of E-boxes located within the
BRCA1
promoter. Consonant with these findings, nuclear Slug and Snail expression are increased in association with BRCA1 repression in a cohort of triple-negative breast cancer patients. Together, these findings establish unique functional links between canonical Wnt signaling, Slug expression, EMT, and BRCA1 regulation.
Selectively altering belief formation in the human brain
Authors: Sharot Tali , Kanai Ryota , Marston David , Korn Christoph W. , Rees Geraint , Dolan Raymond J.
Published: September 2012

Humans form beliefs asymmetrically; we tend to discount bad news but embrace good news. This reduced impact of unfavorable information on belief updating may have important societal implications, including the generation of financial market bubbles, ill preparedness in the face of natural disasters, and overly aggressive medical decisions. Here, we selectively improved people’s tendency to incorporate bad news into their beliefs by disrupting the function of the left (but not right) inferior frontal gyrus using transcranial magnetic stimulation, thereby eliminating the engrained “good news/bad news effect.” Our results provide an instance of how selective disruption of regional human brain function paradoxically enhances the ability to incorporate unfavorable information into beliefs of vulnerability.
Overexpressing mouse model demonstrates the protective role of Muc5ac in the lungs
Authors: Ehre Camille , Worthington Erin N. , Liesman Rachael M. , Grubb Barbara R. , Barbier Diane , O’Neal Wanda K. , Sallenave Jean-Michel , Pickles Raymond J. , Boucher Richard C.
Published: September 2012

MUC5AC, a major gel-forming mucin expressed in the lungs, is secreted at increased rates in response to infectious agents, implying that mucins exert a protective role against inhaled pathogens. However, epidemiological and pathological studies suggest that excessive mucin secretion causes airways obstruction and inflammation. To determine whether increased MUC5AC secretion alone produces airway obstruction and/or inflammation, we generated a mouse model overexpressing Muc5ac mRNA ∼20-fold in the lungs, using the rCCSP promoter. The Muc5ac cDNA was cloned from mouse lungs and tagged internally with GFP. Bronchoalveolar lavage fluid (BALF) analysis demonstrated an approximate 18-fold increase in Muc5ac protein, which formed high-molecular-weight polymers. Histopathological studies and cell counts revealed no airway mucus obstruction or inflammation in the lungs of Muc5ac-transgenic (Muc5ac-Tg) mice. Mucus clearance was preserved, implying that the excess Muc5ac secretion produced an “expanded” rather than more concentrated mucus layer, a prediction confirmed by electron microscopy. To test whether the larger mucus barrier conferred increased protection against pathogens, Muc5ac-Tg animals were challenged with PR8/H1N1 influenza viruses and showed significant decreases in infection and neutrophilic responses. Plaque assay experiments demonstrated that Muc5ac-Tg BALF and purified Muc5ac reduced infection, likely via binding to α2,3-linked sialic acids, consistent with influenza protection in vivo. In conclusion, the normal mucus transport and absence of a pulmonary phenotype in Muc5ac-Tg mice suggests that mucin hypersecretion alone is not sufficient to trigger luminal mucus plugging or airways inflammation/goblet cell hyperplasia. In contrast, increased Muc5ac secretion appears to exhibit a protective role against influenza infection.
Predicting errors from reconfiguration patterns in human brain networks
Authors: Ekman Matthias , Derrfuss Jan , Tittgemeyer Marc , Fiebach Christian J.
Published: September 2012

Task preparation is a complex cognitive process that implements anticipatory adjustments to facilitate future task performance. Little is known about quantitative network parameters governing this process in humans. Using functional magnetic resonance imaging (fMRI) and functional connectivity measurements, we show that the large-scale topology of the brain network involved in task preparation shows a pattern of dynamic reconfigurations that guides optimal behavior. This network could be decomposed into two distinct topological structures, an error-resilient core acting as a major hub that integrates most of the network’s communication and a predominantly sensory periphery showing more flexible network adaptations. During task preparation, core–periphery interactions were dynamically adjusted. Task-relevant visual areas showed a higher topological proximity to the network core and an enhancement in their local centrality and interconnectivity. Failure to reconfigure the network topology was predictive for errors, indicating that anticipatory network reconfigurations are crucial for successful task performance. On the basis of a unique network decoding approach, we also develop a general framework for the identification of characteristic patterns in complex networks, which is applicable to other fields in neuroscience that relate dynamic network properties to behavior.
From simple innate biases to complex visual concepts
Authors: Ullman Shimon , Harari Daniel , Dorfman Nimrod
Published: September 2012

Early in development, infants learn to solve visual problems that are highly challenging for current computational methods. We present a model that deals with two fundamental problems in which the gap between computational difficulty and infant learning is particularly striking: learning to recognize hands and learning to recognize gaze direction. The model is shown a stream of natural videos and learns without any supervision to detect human hands by appearance and by context, as well as direction of gaze, in complex natural scenes. The algorithm is guided by an empirically motivated innate mechanism—the detection of “mover” events in dynamic images, which are the events of a moving image region causing a stationary region to move or change after contact. Mover events provide an internal teaching signal, which is shown to be more effective than alternative cues and sufficient for the efficient acquisition of hand and gaze representations. The implications go beyond the specific tasks, by showing how domain-specific “proto concepts” can guide the system to acquire meaningful concepts, which are significant to the observer but statistically inconspicuous in the sensory input.
The Wingless homolog Wnt5a stimulates phagocytosis but not bacterial killing
Authors: Maiti George , Naskar Debdut , Sen Malini
Published: September 2012

Phagocytosis is a primary defense program orchestrated by monocytes/macrophages. Unregulated phagocytosis can lead to pathological conditions. In the current study we have demonstrated that Wnt5a stimulates phagocytosis through PI3 kinase–Rac1 and lipid-raft-dependent processes. Wnt5a-mediated augmentation in phagocytosis is suppressed by blocking expression of the putative Wnt5a receptor Frizzled 5. Enhanced phagocytosis of bacteria by Wnt5a–Fz5 signaling increases the secretion of proinflammatory cytokines, but not the bacterial killing rate. Furthermore, a small molecule inhibitor of Wnt production, IWP-2, which reduces secretion of functionally active Wnt5a, not only suppresses both phagocytosis and the secretion of proinflammatory cytokines but also accelerates the bacterial killing rate.
Bisphenol A alters early oogenesis and follicle formation in the fetal ovary of the rhesus monkey
Authors: Hunt Patricia A. , Lawson Crystal , Gieske Mary , Murdoch Brenda , Smith Helen , Marre Alyssa , Hassold Terry , VandeVoort Catherine A.
Published: September 2012

Widespread use of the endocrine disrupting chemical bisphenol A (BPA) in consumer products has resulted in nearly continuous human exposure. In rodents, low-dose exposures have been reported to adversely affect two distinct stages of oogenesis in the developing ovary: the events of prophase at the onset of meiosis in the fetal ovary and the formation of follicles in the perinatal ovary. Because these effects could influence the reproductive longevity and success of the exposed individual, we conducted studies in the rhesus monkey to determine whether BPA induces similar disturbances in the developing primate ovary. The routes and levels of human exposure are unclear; hence, two different exposure protocols were used: single daily oral doses and continuous exposure via subdermal implant. Our analyses of second trimester fetuses exposed at the time of meiotic onset suggest that, as in mice, BPA induces subtle disturbances in the prophase events that set the stage for chromosome segregation at the first meiotic division. Our analyses of third-trimester fetuses exposed to single daily oral doses during the time of follicle formation revealed an increase in multioocyte follicles analogous to that reported in rodents. However, two unique phenotypes were evident in continuously exposed animals: persistent unenclosed oocytes in the medullary region and small, nongrowing oocytes in secondary and antral follicles. Because effects on both stages of oogenesis were elicited using doses that yield circulating levels of BPA analogous to those reported in humans, these findings raise concerns for human reproductive health.