Long-term perfusion culture of hybridoma: a "grow or die" cell cycle system

In order to elucidate the hybridoma life cycle and the limiting factors in perfusion systems, we performed cultures in a stirred tank bioreactor, coupled to an external tangential flow filtration unit. Cell density and antibody production in perfusion were consistent with previous studies. The average life span of the cells (2.1-2.2 days), antibody, productivity per cell produced (30-38 mg/10(9) cells) and cell size diameter evolution appeared similar to values observed in batch cultures. These observations highly suggest a similar "grow or die" life cycle. Cell and antibody production, strictly related to the medium perfusion rate, seem to be under the control of the nutrient availability. A hypothesis to explain such a life cycle of hybridoma cells in perfusion systems and a model for viable and dead cell density is proposed.     

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

Background

Untargeted mass spectrometry (MS)-based metabolomics data often contain missing values that reduce statistical power and can introduce bias in biomedical studies. However, a systematic assessment of the various sources of missing values and strategies to handle these data has received little attention. Missing data can occur systematically, e.g. from run day-dependent effects due to limits of detection (LOD); or it can be random as, for instance, a consequence of sample preparation.

Methods

We investigated patterns of missing data in an MS-based metabolomics experiment of serum samples from the German KORA F4 cohort (n?=?1750). We then evaluated 31 imputation methods in a simulation framework and biologically validated the results by applying all imputation approaches to real metabolomics data. We examined the ability of each method to reconstruct biochemical pathways from data-driven correlation networks, and the ability of the method to increase statistical power while preserving the strength of established metabolic quantitative trait loci.

Results

Run day-dependent LOD-based missing data accounts for most missing values in the metabolomics dataset. Although multiple imputation by chained equations performed well in many scenarios, it is computationally and statistically challenging. K-nearest neighbors (KNN) imputation on observations with variable pre-selection showed robust performance across all evaluation schemes and is computationally more tractable.

Conclusion

Missing data in untargeted MS-based metabolomics data occur for various reasons. Based on our results, we recommend that KNN-based imputation is performed on observations with variable pre-selection since it showed robust results in all evaluation schemes.

     

Practice guidelines, patient interests, and risky procedures

A clinical scenario is described where an anaesthetist is concerned about the seemingly high risk/benefit ratio relating to laparoscopic versus standard inguinal hernia operations. Some options for further action by the anaesthetist are introduced. The remainder of the paper explores the question of who can legitimately assess the acceptability of risk/benefit ratios, and defends the use of practice guidelines at the expense of so called clinical freedom. It is argued that respect for persons is not breached by limiting the treatment options offered to patients to those therapies which have a 'reasonable' risk/benefit ratio. This 'reasonableness' is context dependent, and should be properly decided by those with expertise in the field.     

Microsatellite markers used for genome-wide association mapping of partial resistance to <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> in a world collection of <Emphasis Type="Italic">Brassica napus</Emphasis>

The fungal pathogen Sclerotinia sclerotiorum causes stem rot of oilseed rape (Brassica napus) worldwide. In preparation for genome-wide association mapping (GWAM) of sclerotinia resistance in B. napus, 152 accessions from diverse geographical regions were screened with a single Canadian isolate, #321. Plants were inoculated by attaching mycelium plugs to the main stem at full flower. Lesion lengths measured 7, 14 and 21 days after inoculation were used to calculate the area under the disease progress curve (AUDPC). Depth of penetration was noted and used to calculate percent soft and collapsed lesions (% s + c). The two disease traits were highly correlated (r = 0.93). Partially resistant accessions (AUDPC <7 and % s + c <2) were identified primarily from South Korea and Japan with a few from Pakistan, China and Europe. Genotyping of accessions with 84 simple sequence repeat markers provided 690 polymorphic loci for GWAM. The general linear model in TASSEL best fitted the data when adjusted for population structure (STRUCTURE), GLM + Q. After correction for positive false discovery rate, 34 loci were significantly associated with both disease traits of which 21 alleles contributed to resistance, while the remaining enhanced susceptibility. The phenotypic variation explained by the loci ranged from 6 to 25 %. Five loci mapped to published quantitative trait loci conferring sclerotinia resistance in Chinese lines.     

Mate guarding and frequent copulation in birds: A meta‐analysis of their relationship to paternity and male phenotype

In many birds, males are presumed to protect their paternity by closely guarding their mate or copulating frequently with her. Both these costly behaviors are assumed to reduce the risk and/or intensity of sperm competition. However, despite many studies on avian extra‐pair paternity, it remains unclear how strongly these behaviors are related to fitness and other key life‐history traits. Here, we conduct meta‐analyses to address two questions. First, are mate guarding and/or frequent copulation positively correlated with a male's share of paternity at his nest? We find a significant positive correlation between both presumed paternity protection behaviors and paternity share. The relationship is, however, weak (r = 0.08–0.23). This is perhaps unsurprising if the risk of partner infidelity, hence the need to protect paternity, varies among males. For example, more attractive males might have less need to protect their paternity. Second, do males with higher indices of so‐called male “quality” (phenotypic measures, usually subjectively defined by researchers as predictors of male attractiveness) exhibit lower levels of paternity protection behavior? We find a negative correlation between male quality and paternity protection. This finding might partly explain the weak relationship between paternity protection and paternity, although we discuss other, nonmutually exclusive possibilities.     

The role of eddies in the diving behaviour of female southern elephant seals

As the Antarctic Circumpolar Current crosses the South-West Indian Ocean Ridge, it creates an extensive eddy field characterised by high sea level anomaly variability. We investigated the diving behaviour of female southern elephant seals from Marion Island during their post-moult migrations in relation to this eddy field in order to determine its role in the animals’ at-sea dispersal. Most seals dived within the region significantly more often than predicted by chance, and these dives were generally shallower and shorter than dives outside the eddy field. Mixed effects models estimated reductions of 44.33 ± 3.00 m (maximum depth) and 6.37 ± 0.10 min (dive duration) as a result of diving within the region, along with low between-seal variability (maximum depth: 5.5 % and dive duration: 8.4 %). U-shaped dives increased in frequency inside the eddy field, whereas W-shaped dives with multiple vertical movements decreased. Results suggest that Marion Island’s adult female elephant seals’ dives are characterised by lowered cost-of-transport when they encounter the eddy field during the start and end of their post-moult migrations. This might result from changes in buoyancy associated with varying body condition upon leaving and returning to the island. Our results do not suggest that the eddy field is a vital foraging ground for Marion Island’s southern elephant seals. However, because seals preferentially travel through this area and likely forage opportunistically while minimising transport costs, we hypothesise that climate-mediated changes in the nature or position of this region may alter the seals’ at-sea dispersal patterns.