Recombinant protein expression by targeting pre-selected chromosomal loci

Background  

Recombinant protein expression in mammalian cells is mostly achieved by stable integration of transgenes into the chromosomal DNA of established cell lines. The chromosomal surroundings have strong influences on the expression of transgenes. The exploitation of defined loci by targeting expression constructs with different regulatory elements is an approach to design high level expression systems. Further, this allows to evaluate the impact of chromosomal surroundings on distinct vector constructs.     

Effect of fasting on hypogean (<Emphasis Type="Italic">Niphargus stygius</Emphasis>) and epigean (<Emphasis Type="Italic">Gammarus fossarum</Emphasis>) amphipods: a laboratory study

Two amphipods, the hypogean Niphargus stygius and epigean Gammarus fossarum, were analyzed for fatty acid (FA) composition, electron transport system (ETS) activity and respiration (R) during a laboratory fasting experiment. In agreement with ETS and R measurements (and the ETS/R ratio), the hypogean N. stygius utilized FA more slowly than the epigean G. fossarum. Inter-specific differences in the utilization of certain FA during fasting were also revealed. While N. stygius tended to preserve all of its FA during the experimental fasting period, G. fossarum showed a tendency to utilize MUFA (monounsaturated FA) and SAFA (saturated FA) and preferentially retain PUFA (polyunsaturated FA). The significant correlations between ETS activity and composition of specific FA during fasting can be linked to R. During the fasting, both ETS activity and respiration rate of G. fossarum decreased, however, ETS/R ratio increased. In contrast, N. stygius did not show significant changes in these parameters. This is the first report, which connects ETS activity with changes in concentrations of specific FA during fasting. Such evolutionary adaptations of hypogean species enables them to better survive chronically low and/or discontinuous food supplies compared to epigean species, which live in environments where food shortages are much less frequent.     

DNA suspension arrays: silencing discrete artifacts for high-sensitivity applications

Detection of low frequency single nucleotide polymorphisms (SNPs) has important implications in early screening for tumorgenesis, genetic disorders and pathogen drug resistance. Nucleic acid arrays are a powerful tool for genome-scale SNP analysis, but detection of low-frequency SNPs in a mixed population on an array is problematic. We demonstrate a model assay for HIV-1 drug resistance mutations, wherein ligase discrimination products are collected on a suspension array. In developing this system, we discovered that signal from multiple polymorphisms was obscured by two discrete hybridization artifacts. Specifically: 1) tethering of unligated probes on the template DNA elicited false signal and 2) unpredictable probe secondary structures impaired probe capture and suppressed legitimate signal from the array. Two sets of oligonucleotides were used to disrupt these structures; one to displace unligated reporter labels from the bead-bound species and another to occupy sequences which interfered with array hybridization. This artifact silencing system resulted in a mean 21-fold increased sensitivity for 29 minority variants of 17 codons in our model assay for mutations most commonly associated with HIV-1 drug resistance. Furthermore, since the artifacts we characterized are not unique to our system, their specific inhibition might improve the quality of data from solid-state microarrays as well as from the growing number of multiple analyte suspension arrays relying on sequence-specific nucleic acid target capture.     

Phenotypic distribution models corroborate species distribution models: A shift in the role and prevalence of a dominant prairie grass in response to climate change

Phenotypic distribution within species can vary widely across environmental gradients but forecasts of species’ responses to environmental change often assume species respond homogenously across their ranges. We compared predictions from species and phenotype distribution models under future climate scenarios for Andropogon gerardii, a widely distributed, dominant grass found throughout the central United States. Phenotype data on aboveground biomass, height, leaf width, and chlorophyll content were obtained from 33 populations spanning a ~1000 km gradient that encompassed the majority of the species’ environmental range. Species and phenotype distribution models were trained using current climate conditions and projected to future climate scenarios. We used permutation procedures to infer the most important variable for each model. The species‐level response to climate was most sensitive to maximum temperature of the hottest month, but phenotypic variables were most sensitive to mean annual precipitation. The phenotype distribution models predict that A. gerardii could be largely functionally eliminated from where this species currently dominates, with biomass and height declining by up to ~60% and leaf width by ~20%. By the 2070s, the core area of highest suitability for A. gerardii is projected to shift up to ~700 km northeastward. Further, short‐statured phenotypes found in the present‐day short grass prairies on the western periphery of the species’ range will become favored in the current core ~800 km eastward of their current location. Combined, species and phenotype models predict this currently dominant prairie grass will decline in prevalence and stature. Thus, sourcing plant material for grassland restoration and forage should consider changes in the phenotype that will be favored under future climate conditions. Phenotype distribution models account for the role of intraspecific variation in determining responses to anticipated climate change and thereby complement predictions from species distributions models in guiding climate adaptation strategies.     

Ecological tracers reveal resource convergence among prey fish species in a large lake ecosystem

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Variation in male body size and reproductive allocation in the leafcutter ant <Emphasis Type="Italic">Atta colombica</Emphasis>: estimating variance components and possible trade-offs

Remarkably little is known about the traits that determine reproductive success of males in eusocial insects. Their window for mate choice decisions is very short, the actual mating process is very difficult to observe, and their small body sizes have likely prevented systematic studies in many species. In 2008 and 2009, we revisited a Panamanian population of Atta colombica leafcutter ants to partially repeat and complement a study of more than 15 years ago. We compared within- and between-colony variation in male body size (mass and width of head, mesosoma and gaster) and sperm characteristics (length, number and survival after exposure to saline buffer with and without added accessory gland secretion). We also measured the size of accessory glands as the main contributor of seminal fluid and the accessory testes containing all mature sperm, but we found few correlations between these variables. We also obtained little or no evidence for expected trade-offs between sperm number and sperm length and between mesosoma mass and sperm complement, although this could be due to limited sample size and unknown variation in larval resource allocation that was beyond our control. However, we found an interestingly bimodal distribution in broad-sense heritabilities (intra-class correlations) among the variables that we measured. Low heritabilities suggest that mesosoma size (mass and width), accessory testes size, sperm viability (measured as % survival in saline) and probably also accessory gland size are traits directly correlated with reproductive success. However, the much higher heritabilities for total body mass, gaster mass, head width, sperm length and sperm number suggest that these traits are less likely to make direct contributions to male fitness.     

Polyandry reduces sperm length variation in social insects

Postcopulatory sexual selection, either in the form of sperm competition or cryptic female choice, is an important selective force that is thought to have generated the enormous variation in sperm morphology observed interspecifically. However, the evolutionary significance of intraspecific variation in sperm morphology, and the role that postcopulatory sexual selection plays in influencing this variation, remains poorly investigated in invertebrates. Here, we tested the hypothesis that postcopulatory sexual selection reduces variation in sperm morphology, both between and within males, in 27 species of eusocial ants and bees. These eusocial species offer an unusual opportunity to assess how selection acts on variance in sperm morphology, as haploid males produce clonal, haploid sperm that does not experience haploid-diploid conflict. We provide solid evidence that males of polyandrous ant and bee species indeed produce less-variable sperm, indicating that sperm competition selected for sperm of superior quality. Our results offer a mechanistic explanation for the evolution of high-quality sperm and provide comprehensive evidence that sperm morphology of social insects is influenced by sexual selection.     

In vitro fertilization and development of cumulus oocytes complexes collected by ultrasound-guided follicle aspiration in superstimulated llamas

The objective was to evaluate the developmental competence of cumulus-oocyte complexes (COC) collected by follicular aspiration in llamas treated with FSH or eCG. Llamas were assigned randomly to two groups (n = 16 per group) and treated, at the time of ovarian follicular wave emergence, with either: 1) 25 mg of FSH im, twice daily for 4 d; or 2) 1000 IU of eCG as a single i.m. dose. The start of gonadotropin treatment was considered Day 0. Both groups were given 5 mg of Armour Standard LH im on Day 6, and COC were collected by follicle aspiration on Day 7. Expanded COC collected from FSH- (n = 157) and eCG-treated llamas (n = 151) were fertilized in vitro using epididymal sperm, and presumptive zygotes were in vitro cultured in SOF medium for 8 d. The FSH and eCG treatment groups did not differ with respect to: the number of follicles ≥7 mm (16.0 ± 2.7 vs 14.0 ± 1.9, respectively; P = 0.5); the number of COC collected (11.5 ± 1.9 vs 9.7 ± 1.2; P = 0.4); the number of expanded COC (9.8 ± 1.4 vs 9.4 ± 1.2; P = 0.8); or the percentage of presumptive zygotes which developed into 2 to 8 cell stage embryos (65.3 vs 63.1), morulas (46.2 vs 42.5), or blastocysts (23.1 vs 20.5; P > 0.05). In conclusion, FSH and eCG treatments were equally effective for recovery of a high number of expanded COC which were used directly for in vitro fertilization. Furthermore, rate of embryo development was not significantly affected by the gonadotropin treatment used.     

Cdk1 uncouples CtIP-dependent resection and Rad51 filament formation during M-phase double-strand break repair

DNA double-strand break (DSB) resection, which results in RPA-bound single-stranded DNA (ssDNA), is activated in S phase by Cdk2. RPA-ssDNA activates the ATR-dependent checkpoint and homology-directed repair (HDR) via Rad51-dependent mechanisms. On the other hand, the fate of DSBs sustained during vertebrate M phase is largely unknown. We use cell-free Xenopus laevis egg extracts to examine the recruitment of proteins to chromatin after DSB formation. We find that S-phase extract recapitulates a two-step resection mechanism. M-phase chromosomes are also resected in cell-free extracts and cultured human cells. In contrast to the events in S phase, M-phase resection is solely dependent on MRN-CtIP. Despite generation of RPA-ssDNA, M-phase resection does not lead to ATR activation or Rad51 chromatin association. Remarkably, we find that Cdk1 permits resection by phosphorylation of CtIP but also prevents Rad51 binding to the resected ends. We have thus identified Cdk1 as a critical regulator of DSB repair in M phase. Cdk1 induces persistent ssDNA-RPA overhangs in M phase, thereby preventing both classical NHEJ and Rad51-dependent HDR.     

Modeling the relation between cardiac pump function and myofiber mechanics

Complexity of the geometry and structure of the heart hampers easy modeling of cardiac mechanics. The modeling can however be simplified considerably when using the hypothesis that in the normal heart myofiber structure and geometry adapt, until load is evenly distributed. A simple and realistic relationship is found between the hemodynamic variables cavity pressure and volume, and myofiber load parameters stress and strain. The most important geometric parameter in the latter relation is the ratio of cavity volume to wall volume, while actual geometry appears practically irrelevant. Applying the found relationship, a realistic maximum is set to left ventricular pressure after chronic pressure load. Pressures exceeding this level are likely to cause decompensation and heart failure. Furthermore, model is presented to simulate left and right ventricular pump function with left-right interaction.