Historical demographic profiles and genetic variation of the East African Butana and Kenana indigenous dairy zebu cattle

Butana and Kenana breeds from Sudan are part of the East African zebu Bos indicus type of cattle. Unlike other indigenous zebu cattle in Africa, they are unique due to their reputation for high milk production and are regarded as dairy cattle, the only ones of their kind on the African continent. In this study, we sequenced the complete mitochondrial DNA (mtDNA) D‐loop of 70 animals to understand the maternal genetic variation, demographic profiles and history of the two breeds in relation to the history of cattle pastoralism on the African continent. Only taurine mtDNA sequences were identified. We found very high mtDNA diversity but low level of maternal genetic structure within and between the two breeds. Bayesian coalescent‐based analysis revealed different historical and demographic profiles for the two breeds, with an earlier population expansion in the Butana vis a vis the Kenana. The maternal ancestral populations of the two breeds may have diverged prior to their introduction into the African continent, with first the arrival of the ancestral Butana population. We also reveal distinct demographic history between the two breeds with the Butana showing a decline in its effective population size (N_e) in the recent past ~590 years. Our results provide new insights on the early history of cattle pastoralism in Sudan indicative of a large ancient effective population size.     

The potency of tissue-type plasminogen activator (TPA) determined with chromogen and clot-lysis assays

An assessment was made of two methods for determining the potency of tissue-type plasminogen activator (TPA). A chromogenic microtitre plate assay was established which contained TPA, plasminogen, a synthetic plasmin substrate (H-D-valyl-L-leucyl-L-lysyl-p-nitroaniline dihydrochloride, S2251) and any one of the following stimulators: native fibrinogen, enzymatic and chemical digests of fibrinogen, poly-D-lysine (PDL) and chemical derivatives of the latter. The chromogen assay was compared with an automated clot-lysis (turbidimetric) assay for sensitivity, reproducibility and validity for potency determination. Reference preparations of TPA were titrated in both assays: in the chromogen assay the dose-response curves were non-parallel, whereas parallelism was observed in the clot-lysis assay. Thus, the chromogen assay was restricted in its applicability and disqualified from any routine regulatory use. The potency of individual lots of recombinant (r)TPA could only be estimated in International Units (IU) of TPA activity with the automated clot-lysis assay and the potency values obtained (IU/vial) were in remarkably close agreement with the manufacturers' values.     

Phenotype Classification of Zebrafish Embryos by Supervised Learning

Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on supervised machine learning. We show that, compared to manual classification, automatic classification results in 90 to 100% agreement with consensus voting of biological experts in nine out of eleven considered defects in 3 days old zebrafish larvae. Automation of the analysis and classification of zebrafish embryo pictures reduces the workload and time required for the biological expert and increases the reproducibility and objectivity of this classification.     

Refuting phylogenetic relationships

Background  

Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny.     

Mechanosensitive Closed-Closed Transitions in Large Membrane Proteins: Osmoprotection and Tension Damping

Multiconformation membrane proteins are mechanosensitive (MS) if their conformations displace different bilayer areas. Might MS closed-closed transitions serve as tension buffers, that is, as membrane “spandex”? While bilayer expansion is effectively instantaneous, transitions of bilayer-embedded MS proteins are stochastic (thermally activated) so spandex kinetics would be critical. Here we model generic two-state (contracted/expanded) stochastic spandexes inspired by known bacterial osmovalves (MscL, MscS) then suggest experimental approaches to test for spandex-like behaviors in these proteins. Modeling shows: 1), spandex kinetics depend on the transition state location along an area reaction coordinate; 2), increasing membrane concentration of a spandex right-shifts its midpoint (= tension-Boltzmann); 3), spandexes with midpoints below the activating tension of an osmovalve could optimize osmovalve deployment (required: large midpoint, barrier near the expanded state); 4), spandexes could damp bilayer tension excursions (required: midpoint at target tension, and for speed, barrier halfway between the contracted and expanded states; the larger the spandex Δ-area, the more precise the maintenance of target tension; higher spandex concentrations damp larger amplitude strain fluctuations). One spandex species could not excel as both first line of defense for osmovalve partners and tension damper. Possible interactions among MS closed-closed and closed-open transitions are discussed for MscS- and MscL-like proteins.     

An explanatory model to validate the way water activity rules periodic terrace generation in <Emphasis Type="Italic">Proteus mirabilis</Emphasis> swarm

This paper explains the biophysical principles which, according to us, govern the Proteus mirabilis swarm phenomenon. Then, this explanation is translated into a mathematical model, essentially based on partial differential equations. This model is then implemented using numerical methods of the finite volume type in order to make simulations. The simulations show most of the characteristics which are observed in situ and in particular the terrace generation.      

Interspecific differences in drift behaviour between the native <Emphasis Type="Italic">Gammarus pulex</Emphasis> and the exotic <Emphasis Type="Italic">Gammarus roeseli</Emphasis> and possible implications for the invader’s success

“Drifting” is known to subject aquatic invertebrates to intense predation by drift feeding fish. Consequently, interspecific variations in drifting behaviour could lead to differences in predation pressure between coexisting prey species. Predation being an important factor determining the success of invaders, differences in drift patterns could advantage either native or exotic invertebrates through differential predation by native fish predators. The exotic freshwater amphipod (Gammarus roeseli) has now largely colonized Western Europe where it is often found in sympatry with a native species (Gammarus pulex). Here we documented interspecific differences in drifting behaviour that might have favored the invader’s success through differential predation. Benthic and drifting amphipods were sampled three times at the same site to compare the proportion of each species within and between sample types (benthos or drift) across time. Compared with the benthos, where the invader (G. roeseli) was significantly less abundant than the native (G. pulex), G. roeseli was proportionally overrepresented in the drift but displayed a very different drifting pattern. While G. pulex drift rates remained roughly constant over a 24 h period, G. roeseli showed a marked diel periodicity with low diurnal and high nocturnal drift rates. Such drifting behaviour could procure this species with a competitive advantage regarding predation as most drift feeding fish are diurnal. As a result, the native appears more disadvantaged with respect to drift. This may partly explain the ability of G. roeseli to coexist with G. pulex in a habitat more suitable to the native.     

Climate Driven Life Histories: The Case of the Mediterranean Storm Petrel

Seabirds are affected by changes in the marine ecosystem. The influence of climatic factors on marine food webs can be reflected in long-term seabird population changes. We modelled the survival and recruitment of the Mediterranean storm petrel (Hydrobates pelagicus melitensis) using a 21-year mark-recapture dataset involving almost 5000 birds. We demonstrated a strong influence of prebreeding climatic conditions on recruitment age and of rainfall and breeding period conditions on juvenile survival. The results suggest that the juvenile survival rate of the Mediterranean subspecies may not be negatively affected by the predicted features of climate change, i.e., warmer summers and lower rainfall. Based on considerations of winter conditions in different parts of the Mediterranean, we were able to draw inferences about the wintering areas of the species for the first time.     

Effets sur le spermatozoïde humain du Diuron (3-(3,4-dichlorophényl)-1,1-diméthyl-urée) et de l’un de ses produits de transformation, la 3,4-dichloroaniline (3,4-DCA) (Etude préliminaire)

Diuron belongs to the family of halogenophenylureas, one of the main groups of herbicides used for more than 40 years. These herbicides absorb sunlight and can be photochemically transformed in the environment (herbicides are transformed on the soil surface exposed to sunlight) or biotransformed by microorganisms present in soil or in water. The metabolites (chlorohydroxyphenylurea, chlorophenylaniline, respectively) are more toxic than the parent compound, as demonstrated by a bioluminescence inhibition assay performed with a marine bacterium (Vibrio fischeri toxicity test). The lipophilicity of these pesticides makes the cell membrane a target for their action, especially the spermatozoa cell membrane. The aim of this study is to use human spermatozoa to evaluate the effect of this urea pesticide and its biotransformed product on the spermatozoa membrane. We investigated the structural and functional effects of these environmental pollutants on spermatozoa. Three million spermatozoa purified on a 95/47.5% Percoll gradient were suspended in 250 μl of modified Earle’s medium (without phenol red) supplemented with 7.5% of human decomplemented serum. Pesticides (Diuron or 3,4-dichloroaniline (3,4-DCA)) were added at a final concentration of 0.1; 1 and 5 mM. Samples were incubated at room temperature for 24 hours. We show that both Diuron and 3,4-DCA decrease motility and vitality of spermatozoa incubated with the highest concentration of pesticides. Our preliminary results show that the effects are more rapid and more intense with the biotransformed product (3,4-DCA) than with Diuron. Addition of herbicide to human spermatozoa increases membrane fluidity, assessed by measuring the fluorescence polarisation anisotropy with a fluorescent probe: 1,6-diphenyl-1,3,5-hexatriene (DPH). Changes in membrane fluidity may be a primary toxic effect of these herbicides. These results suggest that human spermatozoa may constitute a valuable indicator of the toxic effects of pesticides.