Brachionus leydigii (Monogononta: Ploima) reported from the western basin of Lake Erie.

Several species of non-indigenous planktonic invertebrates have historically been introduced to the Laurentian Great Lakes. Previous introductions of non-indigenous planktonic invertebrates to the Great Lakes have been crustacean zooplankton, specifically Cladocera and Copepoda. This report documents the first known occurrence of Brachionus leydigii var. tridentatus (Zernov, 1901) in Lake Erie and possibly the first detection of a non-indigenous rotifer species in the Laurentian Great Lakes. The specimen was collected from a U.S. EPA monitoring station in the western basin of Lake Erie on April 4, 2016.

Pond sediment magnetite grains show a distinctive microbial community.

Formation of magnetite in anaerobic sediments is thought to be enhanced by the activities of iron-reducing bacteria. Geobacter has been implicated as playing a major role, as in culture its cells are often associated with extracellular magnetite grains. We studied the bacterial community associated with magnetite grains in sediment of a freshwater pond in South Korea. Magnetite was isolated from the sediment using a magnet. The magnetite-depleted fraction of sediment was also taken for comparison. DNA was extracted from each set of samples, followed by PCR for 16S bacterial ribosomal RNA (rRNA) gene and HiSeq sequencing. The bacterial communities of the magnetite-enriched and magnetite-depleted fractions were significantly different. The enrichment of three abundant operational taxonomic units (OTUs) suggests that they may either be dependent upon the magnetite grain environment or may be playing a role in magnetite formation. The most abundant OTU in magnetite-enriched fractions was Geobacter, bolstering the case that this genus is important in magnetite formation in natural systems. Other major OTUs strongly associated with the magnetite-enriched fraction, rather than the magnetite-depleted fraction, include a Sulfuricella and a novel member of the Betaproteobacteria. The existence of distinct bacterial communities associated with particular mineral grain types may also be an example of niche separation and coexistence in sediments and soils, which cannot usually be detected due to difficulties in separating and concentrating minerals.

Bio-processing of macroalgae Palmaria palmata: metabolite fractionation from pressed fresh material and ensiling considerations for long-term storage.

Red algae, belonging to the phylum Rhodophyta, contain an abundance of useful chemicals including bioactive molecules and present opportunities for the production of different products through biorefinery cascades. The rhodophyte Palmaria palmata, commonly termed dulse or dillisk, grows predominantly on the northern coasts of the Atlantic and Pacific Oceans and is a well-known snack food. Due to its abundance, availability and cultivation capacity, P. palmata was selected for study as a potential candidate for a biorefinery process. In addition to studying juice and solid fractions of freshly harvested P. palmata, we have investigated the novel possibility of preserving algal biomass by ensilaging protocols similar to those employed for terrestrial forage crops. In the metabolite partitioning within the solid and liquid fractions following screw-pressing, the majority of the metabolites screened for-water soluble carbohydrates, proteins and amino acids, lipids, pigments, phenolics and antioxidant activity-remained in the solid fraction, though at differing proportions depending on the metabolite, from 70.8% soluble amino acids to 98.2% chlorophyll a and 98.1% total carotenoids. For the ensiling study, screw-pressed P. palmata, with comparative wilted and chopped, and chopped only samples, were ensiled at scale with and without Safesil silage additive. All samples were successfully ensiled after 90 days, with screw-pressing giving lower or equal pH before and after ensiling compared with the other preparations. Of particular note was the effluent volumes generated during ensiling: 26-49% of the fresh weight, containing 16-34% of the silage dry matter. This may be of advantage depending on the final use of the biomass.

The E mu-myc transgenic mouse. A model for high-incidence spontaneous lymphoma and leukemia of early B cells.

Mice transgenic for a c-myc gene driven by the IgH enhancer (E mu-myc) were shown to almost invariably develop lymphomas, 90% succumbing in the first 5 mo of life. The tumors typically presented as rapidly progressive lymphadenopathy with thymic involvement and were highly malignant by transplantation assay. Morphologically, they were lymphoblastic lymphomas, usually accompanied by lymphoid leukemia and granulocytosis, and were distinct from the tumors that arose much later in 37% of nontransgenic mice of the same (C57BL/6 x SJL)F2 genetic background. Cell-surface markers on 31 E mu-myc tumors identified 52% as pre-B lymphomas, 29% as mixed pre-B and B lymphomas, and 19% as B lymphomas. The tumors appeared to arise at random from a population of pre-B cells expanded by constitutive expression of the myc transgene. A majority of the animals initiated malignancy at the rate of 17% per week. The rate at which the cycling, benign pre-B cells spontaneously convert to malignancy was estimated to about 10(-10) per cell per generation. A transient leukocytosis identified in young E mu-myc mice was developed into a rapid assay for inheritance of the transgene.

A search for messenger RNA molecules bearing immunoglobulin VH nucleotide sequences in T cells.

Expression of VH-coded mRNA molecules in T cells, antigen-specific T cell lines, or T cell hybridomas was not detected using four different VH DNA probes under conditions that permitted cross-hybridization between distantly related VH genes. In contrast, VH gene expression was readily detected in two B cell lymphomas and in splenic B cells. Less than one molecule per cell of RNA, exactly complementary to the DNA probes used, would have been detected in these T cell populations. The results thus seriously question the proposition that T cells use the B cell VH repertoire to code for antigen receptors.

In several cell types tumour suppressor p53 induces apoptosis largely via Puma but Noxa can contribute.

The ability of p53 to induce apoptosis in cells with damaged DNA is thought to contribute greatly to its tumour suppressor function. P53 has been proposed to induce apoptosis via numerous transcriptional targets or even by direct cytoplasmic action. Two transcriptional targets shown to mediate its apoptotic role in several cell types encode Noxa and Puma, BH3-only members of the Bcl-2 family. To test if their functions in p53-dependent apoptosis overlap, we generated mice lacking both. These mice develop normally and no tumours have yet arisen. In embryonic fibroblasts, the absence of both Noxa and Puma prevented induction of apoptosis by etoposide. Moreover, following whole body gamma-irradiation, the loss of both proteins protected thymocytes better than loss of Puma alone. Indeed, their combined deficiency protected thymocytes as strongly as loss of p53 itself. These results indicate that, at least in fibroblasts and thymocytes, p53-induced apoptosis proceeds principally via Noxa and Puma, with Puma having the predominant role in diverse cell types. The absence of tumours in the mice suggests that tumour suppression by p53 requires functions in addition to induction of apoptosis.

Degenerative disorders caused by Bcl-2 deficiency prevented by loss of its BH3-only antagonist Bim.

Apoptosis is triggered when proapoptotic members of the Bcl-2 protein family bearing only the BH3 association domain bind to Bcl-2 or its homologs and block their antiapoptotic activity. To test whether loss of the BH3-only protein Bim could prevent the cellular attrition caused by Bcl-2 deficiency, we generated mice lacking both genes. Mice without Bcl-2 have a fragile lymphoid system, become runted, turn gray, and succumb to polycystic kidney disease. Concomitant absence of Bim prevented all these disorders. Indeed, loss of even one bim allele restored normal kidney development, growth, and health. These results demonstrate that Bim levels set the threshold for initiation of apoptosis in several tissues and suggest that degenerative diseases might be alleviated by blocking BH3-only proteins.

Pro-apoptotic apoptosis protease-activating factor 1 (Apaf-1) has a cytoplasmic localization distinct from Bcl-2 or Bcl-x(L).

How Bcl-2 and its pro-survival relatives prevent activation of the caspases that mediate apoptosis is unknown, but they appear to act through the caspase activator apoptosis protease-activating factor 1 (Apaf-1). According to the apoptosome model, the Bcl-2-like proteins preclude Apaf-1 activity by sequestering the protein. To explore Apaf-1 function and to test this model, we generated monoclonal antibodies to Apaf-1 and used them to determine its localization within diverse cells by subcellular fractionation and confocal laser scanning microscopy. Whereas Bcl-2 and Bcl-x(L) were prominent on organelle membranes, endogenous Apaf-1 was cytosolic and did not colocalize with them, even when these pro-survival proteins were overexpressed or after apoptosis was induced. Immunogold electron microscopy confirmed that Apaf-1 was dispersed in the cytoplasm and not on mitochondria or other organelles. After the death stimuli, Bcl-2 and Bcl-x(L) precluded the release of the Apaf-1 cofactor cytochrome c from mitochondria and the formation of larger Apaf-1 complexes, which are steps that presage apoptosis. However, neither Bcl-2 nor Bcl-x(L) could prevent the in vitro activation of Apaf-1 induced by the addition of exogenous cytochrome c. Hence, rather than sequestering Apaf-1 as proposed by the apoptosome model, Bcl-2-like proteins probably regulate Apaf-1 indirectly by controlling upstream events critical for its activation.

Transgenic models of tumor development.

Numerous cancer-prone strains of mice have been created by the introduction of candidate tumor-promoting genes into fertilized eggs. Each transgenic strain is predisposed to develop specific types of tumors, but they usually arise stochastically because of the need for spontaneous mutation of genes that collaborate with the introduced oncogene. These mice are providing insights into the effects of individual oncogenes on cellular proliferation, differentiation, and viability, as well as on oncogene cooperativity. Their predisposed state imposes sensitivity to viral and chemical carcinogenesis, and the mice should prove valuable in tests of potential carcinogens, therapies, and preventive measures.

The Bcl-2 protein family: arbiters of cell survival.

Bcl-2 and related cytoplasmic proteins are key regulators of apoptosis, the cell suicide program critical for development, tissue homeostasis, and protection against pathogens. Those most similar to Bcl-2 promote cell survival by inhibiting adapters needed for activation of the proteases (caspases) that dismantle the cell. More distant relatives instead promote apoptosis, apparently through mechanisms that include displacing the adapters from the pro-survival proteins. Thus, for many but not all apoptotic signals, the balance between these competing activities determines cell fate. Bcl-2 family members are essential for maintenance of major organ systems, and mutations affecting them are implicated in cancer.

Proapoptotic Bcl-2 relative Bim required for certain apoptotic responses, leukocyte homeostasis, and to preclude autoimmunity.

Apoptosis can be triggered by members of the Bcl-2 protein family, such as Bim, that share only the BH3 domain with this family. Gene targeting in mice revealed important physiological roles for Bim. Lymphoid and myeloid cells accumulated, T cell development was perturbed, and most older mice accumulated plasma cells and succumbed to autoimmune kidney disease. Lymphocytes were refractory to apoptotic stimuli such as cytokine deprivation, calcium ion flux, and microtubule perturbation but not to others. Thus, Bim is required for hematopoietic homeostasis and as a barrier to autoimmunity. Moreover, particular death stimuli appear to activate apoptosis through distinct BH3-only proteins.

Mechanical switching of ferroelectric rubber.

At the A to C transition, smectic elastomers have recently been observed to undergo approximately 35% spontaneous shear strains. We first explicitly describe how strains of up to twice this value could be mechanically or electrically induced in Sm-C elastomers by rotation of the director on a cone around the layer normal with an elastic cost dependent on constraints. Second, for typical sample geometries, we give the various microstructures in Sm-C akin to those seen in nematic elastomers under distortions with constraints. It is possible to give explicit results for the nature of the textures. Chiral Sm-C elastomers are ferroelectric. We calculate how the polarization could be mechanically reversed by large, hard, or soft strains of the rubber depending upon sample geometry.

Life-or-death decisions by the Bcl-2 protein family.

In response to intracellular damage and certain physiological cues, cells enter the suicide program termed apoptosis, executed by proteases called caspases. Commitment to apoptosis is typically governed by opposing factions of the Bcl-2 family of cytoplasmic proteins. Initiation of the proteolytic cascade requires assembly of certain caspase precursors on a scaffold protein, and the Bcl-2 family determines whether this complex can form. Its pro-survival members can act by sequestering the scaffold protein and/or by preventing the release of apoptogenic molecules from organelles such as mitochondria. Pro-apoptotic family members act as sentinels for cellular damage: cytotoxic signals induce their translocation to the organelles where they bind to their pro-survival relatives, promote organelle damage and trigger apoptosis.

The Bcl-2 apoptotic switch in cancer development and therapy.

Impaired apoptosis is both critical in cancer development and a major barrier to effective treatment. In response to diverse intracellular damage signals, including those evoked by cancer therapy, the cell's decision to undergo apoptosis is determined by interactions between three factions of the Bcl-2 protein family. The damage signals are transduced by the diverse 'BH3-only' proteins, distinguished by the BH3 domain used to engage their pro-survival relatives: Bcl-2, Bcl-x(L), Bcl-w, Mcl-1 and A1. This interaction ablates pro-survival function and allows activation of Bax and Bak, which commit the cell to apoptosis by permeabilizing the outer membrane of the mitochondrion. Certain BH3-only proteins (e.g. Bim, Puma) can engage all the pro-survival proteins, but others (e.g. Bad, Noxa) engage only subsets. Activation of Bax and Bak appears to require that the BH3-only proteins engage the multiple pro-survival proteins guarding Bax and Bak, rather than binding to the latter. The balance between the pro-survival proteins and their BH3 ligands regulates tissue homeostasis, and either overexpression of a pro-survival family member or loss of a proapoptotic relative can be oncogenic. Better understanding of the Bcl-2 family is clarifying its role in cancer development, revealing how conventional therapy works and stimulating the search for "BH3 mimetics" as a novel class of anticancer drugs.

Mechanical response of smectic-C elastomers.

The elastic response of a smectic-C elastomer to three deformations, namely imposed lambda(xx), lambda(xz), and lambda(zz), has been modeled using a nonlinear theory of a nematic elastomer with embedded smectic layers, and with the director tilt (in the x direction) at a fixed angle with respect to the smectic layer normal (z direction). The main focus is the elastic response after any soft mode of the sample. It is found that the elastomer contracts in the x direction under lambda(xz) shear. On stretching parallel to the layer normal it is found that there is a soft mode that acts to rotate the director toward the z direction. The deformation of the system after this soft mode can be reduced to shear and elongation in the plane of the layers. We make predictions of the mechanical response of the elastomer, in particular the length of the soft plateau and the asymptotic modulus for the elastomer when stretched parallel to the layer normal. Finally, since monodomain Sm-C elastomers are made by the deformation-induced alignment of polydomains, we describe these important systems. Qualitative behavior of the model is then compared to existing experimental literature on the mechanical alignment of polydomains.

Smectic-A elastomers with weak director anchoring.

Experimentally it is possible to manipulate the director in a (chiral) smectic- A elastomer using an electric field. This suggests that the director is not necessarily locked to the layer normal, as described in earlier papers that extended rubber elasticity theory to smectics. Here, we consider the case that the director is weakly anchored to the layer normal assuming that there is a free energy penalty associated with relative tilt between the two. We use a recently developed weak-anchoring generalization of rubber elastic approaches to smectic elastomers and study shearing in the plane of the layers, stretching in the plane of the layers, and compression and elongation parallel to the layer normal. We calculate, inter alia, the engineering stress and the tilt angle between director and layer normal as functions of the applied deformation. For the latter three deformations, our results predict the existence of an instability towards the development of shear accompanied by smectic- C-like order.

Smectic-C tilt under shear in smectic-A elastomers.

Stenull and Lubensky [Phys. Rev. E 76, 011706 (2007)] have argued that shear strain and tilt of the director relative to the layer normal are coupled in smectic elastomers and that the imposition of one necessarily leads to the development of the other. This means, in particular, that a smectic-A elastomer subjected to a simple shear will develop smectic-C-like tilt of the director. Recently, Kramer and Finkelmann [e-print arXiv:0708.2024; Phys. Rev. E 78, 021704 (2008)], performed shear experiments on smectic-A elastomers using two different shear geometries. One of the experiments, which implements simple shear, produces clear evidence for the development of smectic-C-like tilt. Here, we generalize a model for smectic elastomers introduced by Adams and Warner [Phys. Rev. E 71, 021708 (2005)] and use it to study the magnitude of SmC-like tilt under shear for the two geometries investigated by Kramer and Finkelmann. Using reasonable estimates of model parameters, we estimate the tilt angle for both geometries, and we compare our estimates to the experimental results. The other shear geometry is problematic since it introduces additional in-plane compressions in a sheetlike sample, thus inducing instabilities that we discuss.

Transient shear banding in the nematic dumbbell model of liquid crystalline polymers.

In the shear flow of liquid crystalline polymers (LCPs) the nematic director orientation can align with the flow direction for some materials but continuously tumble in others. The nematic dumbbell (ND) model was originally developed to describe the rheology of flow-aligning semiflexible LCPs, and flow-aligning LCPs are the focus in this paper. In the shear flow of monodomain LCPs, it is usually assumed that the spatial distribution of the velocity is uniform. This is in contrast to polymer solutions, where highly nonuniform spatial velocity profiles have been observed in experiments. We analyze the ND model, with an additional gradient term in the constitutive model, using a linear stability analysis. We investigate the separate cases of constant applied shear stress and constant applied shear rate. We find that the ND model has a transient flow instability to the formation of a spatially inhomogeneous flow velocity for certain starting orientations of the director. We calculate the spatially resolved flow profile in both constant applied stress and constant applied shear rate in start up from rest, using a model with one spatial dimension to illustrate the flow behavior of the fluid. For low shear rates flow reversal can be seen as the director realigns with the flow direction, whereas for high shear rates the director reorientation occurs simultaneously across the gap. Experimentally, this inhomogeneous flow is predicted to be observed in flow reversal experiments in LCPs.

Colloidal polymer composites: Are nano-fillers always better for improving mechanical properties?

HYPOTHESIS: Colloidal polymer composites, in which polymer particles are blended with a filler, are widely used in applications including pharmaceuticals, crop protection, inks, and protective coatings. It is generally found that the presence of hard particulate fillers will increase the elastic modulus of a polymer colloid composite. However, the influence of the size of the filler particle on the large-strain deformation and fracture and on the viscoelastic characteristics, including creep, is not well explored. We hypothesize that the size ratio of the filler to the colloidal polymer will play a critical role in determining the properties of the composite. EXPERIMENTS: Colloidal composites were prepared by blending soft polymer colloids (as a binder) with calcium carbonate fillers having four different sizes, spanning from 70 nm to 4.5 µm. There is no bonding between the filler and matrix in the composites. The large-strain deformation, linear viscoelasticity, and creep were determined for each filler size for increasing the filler volume fractions (ϕCC). Weibull statistics were used to analyze the distributions of strains at failure. FINDINGS: We find that the inclusion of nano-fillers leads to brittle fracture at a lower ϕCC than when µm-size fillers are used. The data interpretation is supported by Weibull analysis. However, for a given ϕCC, the storage modulus is higher in the rubbery regime, and the creep resistance is higher when nanoparticles are used. Using scanning electron microscopy to support our arguments, we show that the properties of colloidal composites are correlated with their microstructure, which can be altered through control of the filler:polymer particle size ratio. Hard nanoparticles pack efficiently around larger particles to provide reinforcement (manifested as a higher storage modulus and greater creep resistance), but they also introduce weak points that lead to brittleness.

What cell wall components are the best indicators for Miscanthus digestibility and conversion to ethanol following variable pretreatments?

BACKGROUND: Energy crops including Miscanthus provide a storable, portable energy source which can be used to complement a wide range of products and energy generation systems. Miscanthus is predominantly used in Europe as a combustion material for electricity generation but also has the potential for biochemical conversion due to its high yield and low-nutrient requirements. The ratio of holocellulose (hemicellulose and cellulose combined) to acid detergent lignin (H:L) within the senesced material has previously been shown to indicate the relative suitability of Miscanthus accessions for thermochemical conversion. In this study, the ratio was assessed to examine its use as a selection aid for biochemical conversion. 20 highly-characterised Miscanthus accessions were saccharified using an enzyme mix to determine optimum sugar release. Nine of these accessions spanning high, medium and low H:L ratios were then autoclaved with dilute acid, alkali or water, and enzymically hydrolysed and fermented to produce ethanol. Samples taken throughout the process allowed assessments of released sugars. RESULTS: Enzymic degradation of the biomass showed a relationship between H:L ratio and glucose release, with high glucose release for high H:L ratio accessions and vice versa. Xylose release showed no such relationship. This relationship was maintained following pretreatments and enzyme saccharification, where compound analysis showed that following all pretreatments, accessions with high H:L ratios repeatedly had the highest releases of glucose, xylose and arabinose, and produced more ethanol. Release of all measured compounds increased with the pretreatment severity and ethanol yields from each pretreatment correlated with the respective glucose yield, providing assurance that any inhibitory compounds generated were tolerated by the fermentation yeast. Strong correlations were also seen between glucose release, ethanol and cell wall components, with cellulose showing the highest correlations with ethanol yields for some treatments and H:L ratio with others. CONCLUSIONS: The H:L ratio is a good predictor of ethanol yields and sugar release from Miscanthus in this study but individual components lignin and cellulose also correlate well, especially for hot water and mild acid pretreatments. In conclusion, use of the H:L ratio does not provide any advantages over the concentration of individual cell wall components for predicting sugar release and ethanol yields.