Early plant domestications in southern India: some preliminary archaeobotanical results

Analysis of flotation samples from twelve sites in Karnataka and Andhra Pradesh (south India) provides clear evidence for the predominant subsistence plants of the Neolithic period (2,800–1,200 cal b.c.). This evidence indicates that the likely staples were two pulses (Vigna radiata and Macrotyloma uniflorum) and two millet-grasses (Brachiaria ramosa and Setaria verticillata) which were indigenous to the Indian peninsula. At some sites there is evidence for limited cultivation of wheats (Triticum diococcum, Triticum durum/aestivum) and barley (Hordeum vulgare), and a few crops that originated in Africa, including hyacinth bean (Lablab purpureus), pearl millet (Pennisetum glaucum) and finger millet (Eleusine coracana). In addition there is evidence for cotton (Gossypium sp.), and linseed (Linum sp.), as well as gathered fruits of Ziziphus and two Cucurbitaceae. This evidence suggests that the earliest agriculture in south India, dating to the third millennium b.c., was based on plants domesticated in the region, and that subsequently from the late 3^rd millennium b.c. through the 2^nd millennium additional crops from other regions were adopted into the subsistence system.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00334-004-0036-9     

Effects of shear stress on endothelial cell haptotaxis on micropatterned surfaces

Endothelial cell (EC) migration plays a critical role in vascular remodeling. Here we investigated the interactions between haptotaxis (induced by extracellular matrix gradient) and mechanotaxis (induced by mechanical forces) during EC migration. A micropatterning technique was used to generate step changes of collagen surface density. Due to haptotaxis, ECs developed focal adhesions and migrated into the area with higher surface density of collagen. Different levels of fluid shear stress were applied on ECs in the direction perpendicular to collagen strips. Shear stress at 2 dyn/cm2 did not affect haptotaxis, while shear stress at 3 dyn/cm2 or higher was sufficient to drive the migration of most ECs in the flow direction and against haptotaxis. Immunostaining revealed the increase of focal adhesions and lamellipodial protrusion in the direction of flow. These results suggest that shear stress beyond a certain threshold can be a predominant factor to determine the direction of EC migration.     

Cystic fibrosis allele frequency,sex ratio anomalies and fertility: a new theory for the dissemination of mutant alleles

Summary The observation that mothers of cystic fibrosis patients come from sibships that are larger than those of the fathers is explained by a decrease in sex ratio with increasing size of parental sibships. This feature also provides the basis for a new theory for the dissemination of the major mutant allele, deduced to have arisen 2700–5000 years ago, in accordance with an overall heterozygote advantage of around 3%. In heterozygous women with heterozygous partners, sex-related selection probably occurs after fertilization.     

Behaviorally measured tactile sensitivity in the common bottlenose dolphin,Tursiops truncatus

Little research has been conducted on the somatosensory system of toothed whales and it remains uncertain how tactile sensitivity varies about their bodies. In this study, tactile sensitivity to high-frequency (250-Hz) displacement of the skin was quantified in three trained adult common bottlenose dolphins (Tursiops truncatus) using a vibratory device (tactor). The magnitude of skin displacement was controlled by varying the voltage to the tactor held against the skin surface with a constant force. Tactile thresholds were determined using an adaptive method of limits in which dolphins reported perception of the tactile stimulus by producing a whistle. Displacement thresholds ranged from 2.4 to 40 μm, with the greatest sensitivity found along the rostrum, melon, and blowhole. Sensitivity decreased caudally along the body, with the dorsal fin and tip of the fluke being the least sensitive locations tested. The results support hypotheses that the follicles on the dolphin rostrum are particularly important for perception. The reduction in tactile sensitivity at the appendages is consistent with their primary role in stabilization and locomotion compared to exploration or environmental sensing.     

Genomic BLUP Decoded: A Look into the Black Box of Genomic Prediction

Genomic best linear unbiased prediction (BLUP) is a statistical method that uses relationships between individuals calculated from single-nucleotide polymorphisms (SNPs) to capture relationships at quantitative trait loci (QTL). We show that genomic BLUP exploits not only linkage disequilibrium (LD) and additive-genetic relationships, but also cosegregation to capture relationships at QTL. Simulations were used to study the contributions of those types of information to accuracy of genomic estimated breeding values (GEBVs), their persistence over generations without retraining, and their effect on the correlation of GEBVs within families. We show that accuracy of GEBVs based on additive-genetic relationships can decline with increasing training data size and speculate that modeling polygenic effects via pedigree relationships jointly with genomic breeding values using Bayesian methods may prevent that decline. Cosegregation information from half sibs contributes little to accuracy of GEBVs in current dairy cattle breeding schemes but from full sibs it contributes considerably to accuracy within family in corn breeding. Cosegregation information also declines with increasing training data size, and its persistence over generations is lower than that of LD, suggesting the need to model LD and cosegregation explicitly. The correlation between GEBVs within families depends largely on additive-genetic relationship information, which is determined by the effective number of SNPs and training data size. As genomic BLUP cannot capture short-range LD information well, we recommend Bayesian methods with t-distributed priors.     

Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.     

6-Formylindolo(3,2-b)Carbazole (FICZ) Modulates the Signalsome Responsible for RA-Induced Differentiation of HL-60 Myeloblastic Leukemia Cells

6-Formylindolo(3,2-b)carbazole (FICZ) is a photoproduct of tryptophan and an endogenous high affinity ligand for aryl hydrocarbon receptor (AhR). It was previously reported that, in patient-derived HL-60 myeloblastic leukemia cells, retinoic acid (RA)-induced differentiation is driven by a signalsome containing c-Cbl and AhR. FICZ enhances RA-induced differentiation, assessed by expression of the membrane differentiation markers CD38 and CD11b, cell cycle arrest and the functional differentiation marker, inducible oxidative metabolism. Moreover, FICZ augments the expression of a number of the members of the RA-induced signalsome, such as c-Cbl, Vav1, Slp76, PI3K, and the Src family kinases Fgr and Lyn. Pursuing the molecular signaling responsible for RA-induced differentiation, we characterized, using FRET and clustering analysis, associations of key molecules thought to drive differentiation. Here we report that, assayed by FRET, AhR interacts with c-Cbl upon FICZ plus RA-induced differentiation, whereas AhR constitutively interacts with Cbl-b. Moreover, correlation analysis based on the flow cytometric assessment of differentiation markers and western blot detection of signaling factors reveal that Cbl-b, p-p38α and pT390-GSK3β, are not correlated with other known RA-induced signaling components or with a phenotypic outcome. We note that FICZ plus RA elicited signaling responses that were not typical of RA alone, but may represent alternative differentiation-driving pathways. In clusters of signaling molecules seminal to cell differentiation, FICZ co-administered with RA augments type and intensity of the dynamic changes induced by RA. Our data suggest relevance for FICZ in differentiation-induction therapy. The mechanism of action includes modulation of a SFK and MAPK centered signalsome and c-Cbl-AhR association.     

The deubiquitinating enzyme AMSH1 is required for rhizobial infection and nodule organogenesis in Lotus japonicus

Legume–rhizobium symbiosis contributes large quantities of fixed nitrogen to both agricultural and natural ecosystems. This global impact and the selective interaction between rhizobia and legumes culminating in development of functional root nodules have prompted detailed studies of the underlying mechanisms. We performed a screen for aberrant nodulation phenotypes using the Lotus japonicus LORE1 insertion mutant collection. Here, we describe the identification of amsh1 mutants that only develop small nodule primordia and display stunted shoot growth, and show that the aberrant nodulation phenotype caused by LORE1 insertions in the Amsh1 gene may be separated from the shoot phenotype. In amsh1 mutants, rhizobia initially became entrapped in infection threads with thickened cells walls. Some rhizobia were released into plant cells much later than observed for the wild‐type; however, no typical symbiosome structures were formed. Furthermore, cytokinin treatment only very weakly induced nodule organogenesis in amsh1 mutants, suggesting that AMSH1 function is required downstream of cytokinin signaling. Biochemical analysis showed that AMSH1 is an active deubiquitinating enzyme, and that AMSH1 specifically cleaves K63‐linked ubiquitin chains. Post‐translational ubiquitination and deubiquitination processes involving the AMSH1 deubiquitinating enzyme are thus involved in both infection and organogenesis in Lotus japonicus.     

Epigenomic stability assessment during cryopreservation and physiology among various strains of Chromochloris zofingiensis (Chlorophyceae) and their genetic variability revealed by AFLP and MS-AFLP

Chromochloris zofingiensis (Dönz) Fucíková & L.A.Lewis, due to its production of highly valuable carotenoids such as astaxanthin, is a model organism in biotechnology. Since the recognition of this physiological property, many biotechnological applications have only used a single strain (SAG 211-14 = CCAP 211/14 = UTEX 32 = ATCC 30412) to produce biomass and carotenoids. However, multiple acquisitions of strains putatively belonging to the same species raised the question of the conspecificity of those strains and their properties. In this study, the conspecificity of the available strains, which are deposited axenically in SAG, was tested using SSU and ITS rDNA sequencing and AFLP (EcoRI/PstI) analyses. The comparison of SSU and ITS rDNA sequences as well as the AFLP patterns revealed that the investigated strains formed two very similar groups, (1) SAG 211-14, SAG 4.80, SAG 31.80, and SAG 34.80 and (2) SAG 221-2. All strains belonged to one species, C. zofingiensis, and represented one monophyletic lineage within the so-called DO-group of the Chlorophyceae. The robustness to cryopreservation and the subsequent epigenetic variability was detected using the methylation-sensitive AFLP (EcoRI/MspI and EcoRI/HpaII) among the five Chromochloris strains. All strains showed a high rate of survival (54.4–98.1%) during cryopreservation. The methylation patterns varied between precryo and postcryo in all strains detected among three time points (before, shortly after, and 8 weeks after cryopreservation), showing that the MS-AFLP technique has the potential to detect epigenetic effects occurring in response to cryopreservation and other stresses. Finally, the potential of these five strains for usage in biotechnological applications was proven by growing them in aerated cultures with and without additional carbon dioxide supply. The comparison showed that all strains produced high amounts of biomass and carotenoids under aeration with additional CO₂ and were therefore suitable in biotechnology.