The Role of Hydrogen Bond in Designing Molecular Optical Materials

In this perspective article, we revise some of the empirical and semi-empirical strategies for predicting how hydrogen bonding affects molecular and atomic polarizabilities in aggregates. We use p-nitroaniline and hydrated oxalic acid as working examples to illustrate the enhancement of donor and acceptor functional-group polarizabilities and their anisotropy. This is significant for the evaluation of electrical susceptibilities in crystals; and the properties derived from them like the refractive indices.

The Interstellar Neutral He haze in the heliosphere: what can we learn?

Neutral interstellar helium has been observed by the Interstellar Boundary Explorer (IBEX) since 2009, with a signal-to-noise ratio well above 1000. Because of the geometry of the observations, the signal observed from January to March each year is the easiest to identify. However, as we show via simulations, the portion of the signal in the range of intensities from 10(-3) to 10(-2) of the peak value, previously mostly left out from the analysis, may provide important information about the details of the distribution function of interstellar He gas in front of the heliosphere. In particular, these observations may inform us about possible departures of the parent interstellar He population from equilibrium. We compare the expected distribution of the signal for the canonical assumption of a single Maxwell-Boltzmann population with the distributions for a superposition of the Maxwell-Boltzmann primary population and the recently discovered Warm Breeze, and for a single primary population given by a kappa function. We identify the regions on the sky where the differences between those cases are expected to be the most visible against the background. We discuss the diagnostic potential of the fall peak of the interstellar signal, reduced by a factor of 50 due to the Compton-Getting effect but still above the detection limit of IBEX. We point out the strong energy dependence of the fall signal and suggest that searching for this signal in the data could bring an independent assessment of the low-energy measurement threshold of the IBEX-Lo sensor.

Temporal and small-scale spatial variation in grassland productivity, biomass quality, and nutrient limitation

Characterization of spatial and temporal variation in grassland productivity and nutrition is crucial for a comprehensive understanding of ecosystem function. Although within-site heterogeneity in soil and plant properties has been shown to be relevant for plant community stability, spatiotemporal variability in these factors is still understudied in temperate grasslands. Our study aimed to detect if soil characteristics and plant diversity could explain observed small-scale spatial and temporal variability in grassland productivity, biomass nutrient concentrations, and nutrient limitation. Therefore, we sampled 360 plots of 20 cm × 20 cm each at six consecutive dates in an unfertilized grassland in Southern Germany. Nutrient limitation was estimated using nutrient ratios in plant biomass. Absolute values of, and spatial variability in, productivity, biomass nutrient concentrations, and nutrient limitation were strongly associated with sampling date. In April, spatial heterogeneity was high and most plots showed phosphorous deficiency, while later in the season nitrogen was the major limiting nutrient. Additionally, a small significant positive association between plant diversity and biomass phosphorus concentrations was observed, but should be tested in more detail. We discuss how low biological activity e.g., of soil microbial organisms might have influenced observed heterogeneity of plant nutrition in early spring in combination with reduced active acquisition of soil resources by plants. These early-season conditions are particularly relevant for future studies as they differ substantially from more thoroughly studied later season conditions. Our study underlines the importance of considering small spatial scales and temporal variability to better elucidate mechanisms of ecosystem functioning and plant community assembly.

Environmental correlates of species rank − abundance distributions in global drylands

Theoretical models predict lognormal species abundance distributions (SADs) in stable and productive environments, with log-series SADs in less stable, dispersal driven communities. We studied patterns of relative species abundances of perennial vascular plants in global dryland communities to: (i) assess the influence of climatic and soil characteristics on the observed SADs, (ii) infer how environmental variability influences relative abundances, and (iii) evaluate how colonisation dynamics and environmental filters shape abundance distributions. We fitted lognormal and log-series SADs to 91 sites containing at least 15 species of perennial vascular plants. The dependence of species relative abundances on soil and climate variables was assessed using general linear models. Irrespective of habitat type and latitude, the majority of the SADs (70.3%) were best described by a lognormal distribution. Lognormal SADs were associated with low annual precipitation, higher aridity, high soil carbon content, and higher variability of climate variables and soil nitrate. Our results do not corroborate models predicting the prevalence of log-series SADs in dryland communities. As lognormal SADs were particularly associated with sites with drier conditions and a higher environmental variability, we reject models linking lognormality to environmental stability and high productivity conditions. Instead our results point to the prevalence of lognormal SADs in heterogeneous environments, allowing for more evenly distributed plant communities, or in stressful ecosystems, which are generally shaped by strong habitat filters and limited colonisation. This suggests that drylands may be resilient to environmental changes because the many species with intermediate relative abundances could take over ecosystem functioning if the environment becomes suboptimal for dominant species.

Gibberellin Deficiency Confers Both Lodging and Drought Tolerance in Small Cereals

Tef [Eragrostis tef (Zucc.) Trotter] and finger millet [Eleusine coracana Gaertn] are staple cereal crops in Africa and Asia with several desirable agronomic and nutritional properties. Tef is becoming a life-style crop as it is gluten-free while finger millet has a low glycemic index which makes it an ideal food for diabetic patients. However, both tef and finger millet have extremely low grain yields mainly due to moisture scarcity and susceptibility of the plants to lodging. In this study, the effects of gibberellic acid (GA) inhibitors particularly paclobutrazol (PBZ) on diverse physiological and yield-related parameters were investigated and compared to GA mutants in rice (Oryza sativa L.). The application of PBZ to tef and finger millet significantly reduced the plant height and increased lodging tolerance. Remarkably, PBZ also enhanced the tolerance of both tef and finger millet to moisture deficit. Under moisture scarcity, tef plants treated with PBZ did not exhibit drought-related symptoms and their stomatal conductance was unaltered, leading to higher shoot biomass and grain yield. Semi-dwarf rice mutants altered in GA biosynthesis, were also shown to have improved tolerance to dehydration. The combination of traits (drought tolerance, lodging tolerance and increased yield) that we found in plants with altered GA pathway is of importance to breeders who would otherwise rely on extensive crossing to introgress each trait individually. The key role played by PBZ in the tolerance to both lodging and drought calls for further studies using mutants in the GA biosynthesis pathway in order to obtain candidate lines which can be incorporated into crop-breeding programs to create lodging tolerant and climate-smart crops.

Mechanism of damage sensing and cell killing following the inhibition of nucleotide excision repair by fludarabine in quiescent cells

Inhibition of DNA repair by the nucleoside of fludarabine (F-ara-A) induces toxicity in quiescent human cells. The sensing and signaling mechanisms following DNA repair inhibition by F-ara-A are unknown. The central hypothesis of this project was that the mechanistic interaction of a DNA repair initiating agent and a nucleoside analog initiates an apoptotic signal in quiescent cells. The purpose of this research was to identify the sensing and signaling mechanism(s) that respond to DNA repair inhibition by F-ara-A. Lymphocytes were treated with F-ara-A, to accumulate the active triphosphate metabolite and subsequently DNA repair was activated by UV irradiation. Pre-incubation of lymphocytes with 3 μM F-ara-A inhibited DNA repair initiated by 2 J/m2 UV and induced greater than additive apoptosis after 24 h. Blocking the incorporation of F-ara-A nucleotide into repairing DNA using 30 μM aphidicolin considerably lowered the apoptotic response. ^ Wild-type quiescent cells showed a significant loss in viability than did cells lacking functional sensor kinase DNA-PKcs or p53 as measured by colony formation assays. The functional status of ATM did not appear to affect the apoptotic outcome. Immunoprecipitation studies showed an interaction between the catalytic sub-unit of DNA-PK and p53 following DNA repair inhibition. Confocal fluorescence microscopy studies have indicated the localization pattern of p53, DNA-PK and γ-H2AX in the nucleus following DNA damage. Foci formation by γ-H2AX was seen as an early event that is followed by interaction with DNA-PKcs. p53 serine-15 phosphorylation and accumulation were detected 2 h after treatment. Fas/Fas ligand expression increased significantly after repair inhibition and was dependent on the functional status of p53. Blocking the interaction between Fas and Fas ligand by neutralizing antibodies significantly rescued the apoptotic fraction of cells. ^ Collectively, these results suggest that incorporation of the nucleoside analog into repair patches is critical for cytotoxicity and that the DNA damage, while being sensed by DNA-PK, may induce apoptosis by a p53-mediated signaling mechanism. Based on the results, a model is proposed for the sensing of F-ara-A-induced DNA damage that includes γ-H2AX, DNA-PKcs, and p53. Targeting the cellular DNA repair mechanism can be a potential means of producing cytotoxicity in a quiescent population of neoplastic cells. These results also provide mechanistic support for the success of nucleoside analogs with cyclophosphamide or other agents that initiate excision repair processes, in the clinic. ^

Calcium mobilization from the endoplasmic reticulum to the mitochondria during apoptosis in prostate cancer

Previous studies have implicated Ca2+ fluxes in the control of apoptosis but their exact roles in regulating the process remain obscure. Because Ca2+ can serve as a signal for cytochrome c release from isolated mitochondria, we hypothesized that alterations in intracellular Ca2+ compartmentalization might serve as a release signal in whole cells undergoing apoptosis. Exposure of human PC-3 prostate adenocarcinoma cells to staurosporine or DNA damaging agent (doxorubicin) but not to anti-Fas antibody led to early release of Ca2+ from the endoplasmic reticulum and subsequent accumulation of Ca2+ within mitochondria. Both events were blocked in cells stably transfected with Bcl-2 but were not affected by treatment with the pancaspase inhibitor, zVADfmk. The effects of staurosporine were associated with re-localization of Bax from the cytosol to both endoplasmic reticular and mitochondrial membranes. Neither ER Ca 2+ pool depletion nor mitochondrial Ca2+ uptake were observed in DU-145 cells that possess a frameshift mutation in the Bax gene unless wild-type Bax was restored via adenoviral gene transfer. Cytochrome c release and downstream features of apoptosis were attenuated by treatment with an inhibitor of mitochondria) Ca2+ uptake (RU-360). Although, direct pharmacological ER Ca2+ pool emptying in cells treated with thapsigargin did not lead to early cytochrome c release, pretreatment of cells with staurosporine dramatically sensitized mitochondria to thapsigargin-induced cytochrome c release. Together, our data demonstrate that ER-to-mitochondrial Ca2+ fluxes promote cytochrome c release and apoptosis in cells exposed to some (but not all) pro-apoptosic stimuli. ^

SFRP4 regulation of Wnt7a signaling and cellular proliferation in the endometrium

In the endometrium, hormonal effects on epithelial cells are often elicited through stromal hormone receptors via unknown paracrine mechanisms. Several lines of evidence support the hypothesis that Wnts participate in stromal-epithelial cell communication and thus mediate hormone action. Characterization of specific Wnt signaling components in the endometrium was performed using cellular localization studies and evaluating hormone effects in a rat model. Wnt7a was expressed in the luminal epithelium, whereas the extracellular Wnt modulator, SFRP4, was localized to the endometrial stroma. SFRP4 expression is significantly decreased in endometrial carcinoma and aberrant Wnt7a signaling has been shown to cause uterine defects and contribute to the onset of disease. The specific Fzds and SFRPs that bind Wnt7a and the particular signal transduction pathway each Wnt7a-Fzd pair activates have not been identified. Additionally, the function of Wnt7a and SFRP4 in the endometrium has not been addressed. A survey of all Wnt signaling proteins expressed in the endometrium was conducted and Fzd5 and Fzd10 were identified as two receptors capable of transducing the Wnt7a signal. Biologically active recombinant Wnt7a and SFRP4 proteins were purified for quantitative biochemical studies. In Ishikawa cells, Wnt7a binding to Fzd5 activated β-catenin/canonical Wnt signaling and increased cellular proliferation. Wnt7a signaling mediated by Fzd10 induced a non-canonical/JNK-responsive pathway. SFRP4 suppressed Wnt7a action in both an autocrine and paracrine manner. Treatment with SFRP4 protein and overexpression of SFRP4 inhibited endometrial cancer cell growth and induced apoptosis in vitro. A split-eGFP complementation assay was developed to visually detect Wnt7a-Fzd interactions and subsequent pathway activation in cells. By employing a unique ELISA-based protein-protein binding technique, it was demonstrated that Wnt7a binds to SFRP4 and Fzd5 with equal nanomolar affinity. The development of these novel biological tools could lead to a better understanding of Wnt-protein interactions and the identification of new modulators of Wnt signaling. This study supports a mechanism by which the nature of the Wnt7a signal in the endometrium is dependent upon the Fzd repertoire of the cell and can be regulated by SFRP4. The potential tumor suppressor function of SFRP4 suggests it may serve as a therapeutic target for endometrial carcinoma. ^

The SasS -SasR two-component signal transduction system required for early Myxococcus xanthus multicellular *development

Initiation of Myxococcus xanthus multicellular development requires both nutrient limitation and high cell density. The extracellular signal, A signal, which consists of a set of amino acids at specific concentrations, serves as a cell density signal in M. xanthus early development. A reporter gene, designated 4521, that requires both starvation and A signal for developmental expression was used to identify mutations in the signal transduction pathways. A group of point mutations located in the chromosomal sasB locus that bypasses both requirements was previously isolated. One of these point mutations, sasB7, was mapped to the sasS gene, which is predicted to encode a transmembrane histidine protein kinase required for normal development. SasS is a positive regulator of 4521 and a candidate A signal sensor. This dissertation continues the characterization of the sasB locus, focusing on the sasR gene and the functional relationship of SasS and SasR. ^ The sasR gene is located 2.2-kb downstream of sasS. It is predicted to encode an NtrC-like response regulator, which belongs to the family of sigma54 transcriptional activators. SasR is a positive regulator of 4521 gene and is required for normal development. The sasR mutant displays phenotypes similar to that of sasS mutant. Both SasS and SasR are required for the A-signal-dependent 4521 expression. Genetic epistasis analysis indicates that SasR functions downstream of SasS. Biochemical studies show that SasS has autokinase activity, and phosphorylated SasS is able to transfer its phosphate to SasR. We propose that SasS and SasR form a two-component signal transduction system in the A signal transduction pathway. ^ To search for the genes regulated by SasS and SasR, expression patterns of a group of developmental genes were compared in wild-type and sasS null mutant backgrounds. SasS and SasR were found to positively regulate sasN and 4521. The sasN gene was previously identified as a negative regulator of 4521, located at about 170-bp downstream of sasR. It is required for normal fruiting body development. Based on the above data, a regulatory network consisting of sasS, sasR, sasN, and 4521 is hypothesized, and the interactions of the components in this network can now be further studied. ^

Miocene-Pliocene record of Pollen, charcoal and carbon isotopes of plant waxes of ODP Hole 175-1081A

Modern savannah grasslands were established during the late Miocene and Pliocene (8-3 million years ago). In the tropics, grasslands are dominated by grasses that use the C4 photosynthetic pathway, rather than the C3 pathway. The C4 pathway is better adapted to warm, dry and low-CO2 conditions, leading to suggestions that declining atmospheric CO2 levels, increasing aridity and enhanced rainfall seasonality allowed grasses using this pathway to expand during this interval. The role of fire in C4 expansion may have been underestimated. Here we use analyses of pollen, microscopic charcoal and the stable isotopic composition of plant waxes from a marine sediment core off the coast of Namibia to reconstruct the relative timing of changes in plant composition and fire activity for the late Miocene and Pliocene. We find that in southwestern Africa, the expansion of C4 grasses occurred alongside increasing aridity and enhanced fire activity. During further aridification in the Pliocene, the proportion of C4 grasses in the grasslands increased, while the grassland contracted and deserts and semi-deserts expanded. Our results are consistent with the hypothesis that ecological disturbance by fire was an essential feedback mechanism leading to the establishment of C4 grasslands in the Miocene and Pliocene.

CaCO3, foraminifer fragmentation, benthic carbon isotopes, coarse lithic counts and radiogenic isotopes (Sr, Nd, Pb) of the Pliocene and earliest Pleistocene terrigenous component (3.3-2.4 Ma) of IODP Site 306-U1313

We present Plio-Pleistocene records of sediment color, %CaCO3, foraminifer fragmentation, benthic carbon isotopes (d13C) and radiogenic isotopes (Sr, Nd, Pb) of the terrigenous component from IODP Site U1313, a reoccupation of benchmark subtropical North Atlantic Ocean DSDP Site 607. We show that (inter)glacial cycles in sediment color and %CaCO3 pre-date major northern hemisphere glaciation and are unambiguously and consistently correlated to benthic oxygen isotopes back to 3.3 million years ago (Ma) and intermittently so probably back to the Miocene/Pliocene boundary. We show these lithological cycles to be driven by enhanced glacial fluxes of terrigenous material (eolian dust), not carbonate dissolution (the classic interpretation). Our radiogenic isotope data indicate a North American source for this dust (~3.3-2.4 Ma) in keeping with the interpreted source of terrestrial plant wax-derived biomarkers deposited at Site U1313. Yet our data indicate a mid latitude provenance regardless of (inter)glacial state, a finding that is inconsistent with the biomarker-inferred importance of glaciogenic mechanisms of dust production and transport. Moreover, we find that the relation between the biomarker and lithogenic components of dust accumulation is distinctly non-linear. Both records show a jump in glacial rates of accumulation from Marine Isotope Stage, MIS, G6 (2.72 Ma) onwards but the amplitude of this signal is about 3-8 times greater for biomarkers than for dust and particularly extreme during MIS 100 (2.52 Ma). We conclude that North America shifted abruptly to a distinctly more arid glacial regime from MIS G6, but major shifts in glacial North American vegetation biomes and regional wind fields (exacerbated by the growth of a large Laurentide Ice Sheet during MIS 100) likely explain amplification of this signal in the biomarker records. Our findings are consistent with wetter-than-modern reconstructions of North American continental climate under the warm high CO2 conditions of the Early Pliocene but contrast with most model predictions for the response of the hydrological cycle to anthropogenic warming over the coming 50 years (poleward expansion of the subtropical dry zones).

Ice-rafted debris record in the Prydz Bay

Ice-rafted debris mass accumulation rates (IRD MAR) at a drill site on the Antarctic continental margin are investigated to evaluate the linkages between East Antarctic Ice Sheet extent and Southern Ocean temperatures in the early to mid-Pliocene. ODP Site 1165 is within 400 km of the Antarctic coastline and in the direct pathway of icebergs released by the Amery Ice Shelf. The Amery Ice Shelf is the largest ice shelf in East Antarctica and it buttresses the Lambert Glacier drainage system, which accounts for 14% of the outflow from the East Antarctic Ice Sheet. IRD MAR were low during peak Southern Ocean warming in the early Pliocene. After a brief precursor, a tenfold increase in IRD MAR at 3.3 Ma marks the termination of the early Pliocene ice sheet minimum, coincident with the M2 glacial. For the mid-Pliocene, a strong correlation exists between the high-amplitude signal in the LR04 benthic stack and IRD MAR, suggesting linkages between East Antarctic ice extent, global ice volume and deep-water temperatures. The IRD record at Site 1165 provides evidence of greater sensitivity of the Lambert Glacier-Amery Ice Shelf system to Southern Ocean warming than is currently predicted by ice sheet models, which may relate to uncertainties in the understanding of ocean heat uptake, poleward heat transport and ice sheet-ocean interactions.

Flower and seed biomass, and germination rate of arctic tundra plants in response to long term experimental warming

We provide new information on changes in tundra plant sexual reproduction in response to long-term (12 years) experimental warming in the High Arctic. Open-top chambers (OTCs) were used to increase growing season temperatures by 1-2 °C across a range of vascular plant communities. The warming enhanced reproductive effort and success in most species; shrubs and graminoids appeared to be more responsive than forbs. We found that the measured effects of warming on sexual reproduction were more consistently positive and to a greater degree in polar oasis compared with polar semidesert vascular plant communities. Our findings support predictions that long-term warming in the High Arctic will likely enhance sexual reproduction in tundra plants, which could lead to an increase in plant cover. Greater abundance of vegetation has implications for primary consumers - via increased forage availability, and the global carbon budget - as a function of changes in permafrost and vegetation acting as a carbon sink. Enhanced sexual reproduction in Arctic vascular plants may lead to increased genetic variability of offspring, and consequently improved chances of survival in a changing environment. Our findings also indicate that with future warming, polar oases may play an important role as a seed source to the surrounding polar desert landscape.