Influence of day length and temperature on number of main stem leaves and time to flowering in lupin

A growth chamber experiment was carried out to investigate the influence of day length and temperature on the development of flowering in eight varieties of the three grain lupin species Lupinus albus (Wat and C3396), L. angustifolius (Gungurru, Polonez and W26) and L. luteus, (Juno, Radames and Teo). The plants were grown at two temperatures, 10°C and 18°C, in combination with five daylength regimes: 10, 14, 18, 24 h day at full light intensity and 10 h full light extended with 8 h low intensity light. Increased daylength decreased days from sowing to flowering in all varieties, but had little effect on thermal time to flowering in most varieties. However, C3396, W26 and Radames had a significantly longer thermal time to flowering at high, non‐vernalising temperature (18°C) at short daylengths. Low light intensity daylength extension did not significantly influence thermal time to flowering. For flower initiation, measured as number of leaves on the main stem three types of response were found. All varieties formed fewer leaves on the main stem at 10°C than at 18°C, although the two thermo‐neutral varieties of L. luteus, Juno and Teo, gave only a small response to temperature and daylength. In Polonez, Gungurru and Wat, low temperature decreased leaf number, but there was only a small response to changes in daylength. Three varieties, C3396, W26 and Radames, showed longer thermal time to flowering at 18°C with short daylengths. This could be explained by a greater number of main stem leaves formed at short daylength at non‐vernalising temperatures. Increased daylength decreased leaf number in these varieties, but never to a smaller number than for plants grown at 10°C. In these varieties, low intensity extension of the daylength had a similar (W26, Radames) or decreased (C3396) effect compared to full light extension. The hastening of time to flowering by long days could be separated into two effects: a high light energy effect hastened development by increasing the rate of leaf appearance in all varieties, while low light energy in thermo‐sensitive varieties was able to substitute for vernalisation by decreasing leaf number.     

Experimental evidence of the grazing impact of <Emphasis Type="Italic">Boeckella poppei</Emphasis> on phytoplankton in a maritime Antarctic lake

The zooplankton biomass of Lake Boeckella (Hope Bay, Antarctic Peninsula) is strongly dominated by the calanoid copepod Boeckella poppei Mrázek. This work analyses the grazing impact of this copepod on the two dominant fractions of phytoplankton, pico- and nanoplankton, and on the bacterioplankton. By means of in-situ experiments using microcosms, the following hypotheses were tested: (a) the early stages of the copepod mainly graze on phytoplankton; (b) the pre-adult and adult stages graze on phytoplankton and benthic algae. Copepods were separated into two groups of maturity: early stages, and pre-adult and adult stages. The following treatments were performed: (1) only nano- and picoplankton, (2) nano- and picoplankton+periphyton, and (3) only periphyton, for each one of the two copepod maturity groups, and (4) control (without copepods). The variation in nano-phytoplankton density was analysed after 2 and 4 days. The results determined a significant grazing on the nano-phytoplankton fraction in all microcosms containing copepods of both maturity groups (P<0.01). The effect on the nano-phytoplankton was greater when the copepods did not have another source of food (P<0.01). No significant differences between the maturity groups were observed (P>0.05). We also conclude that the copepods use the periphyton as an alternative source of food, which was corroborated by the analysis of gut content. In general, no significant differences among treatments were recorded for the pico-sized fraction (pico-phytoplankton and bacterioplankton), which would suggest that no direct grazing on this fraction exists.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Comparative behaviour of two species of Lepadogaster (Pisces: Gobiesocidae) living at different depths

The two clingfish species studied occupied similar habitats but occurred at different depths. When compared with the subtidal species Lepadogaster candollei , the intertidal species Lepadogaster l. purpurea was less active, spent more time in shelters, visited fewer shelters, showed more site fidelity, and spent less time swimming. Feeding, swimming, and agonistic behaviours were performed mainly in close contact with the substrate in this species. It is hypothesized that these contrasts in behaviour may have evolved under different levels of turbulence.     

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species

Background

Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how expression of parental gene copies (homeologs) responds following genome merger. High throughput RNA sequencing now makes this analysis technically feasible, but tools to determine homeolog expression are still in their infancy.

Results

Here we present HyLiTE – a single-step analysis to obtain tables of homeolog expression in a hybrid or allopolyploid and its parent species directly from raw mRNA sequence files. By implementing on-the-fly detection of diagnostic parental polymorphisms, HyLiTE can perform SNP calling and read classification simultaneously, thus allowing HyLiTE to be run as parallelized code. HyLiTE accommodates any number of parent species, multiple data sources (including genomic DNA reads to improve SNP detection), and implements a statistical framework optimized for genes with low to moderate expression.

Conclusions

HyLiTE is a flexible and easy-to-use program designed for bench biologists to explore patterns of gene expression following genome merger. HyLiTE offers practical advantages over manual methods and existing programs, has been designed to accommodate a wide range of genome merger systems, can identify SNPs that arose following genome merger, and offers accurate performance on non-model organisms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0433-8) contains supplementary material, which is available to authorized users.     

Vocal Behavior During Territorial Intrusions in the Lusitanian Toadfish: Boatwhistles Also Function as Territorial ‘Keep‐Out’ Signals

Male signals are frequently studied in a single behavioral context, but in some cases they may assist multiple functions, namely for both male–male competition and female mate choice. Boatwhistles are known as the mate attraction calls of toadfishes typically produced during the breeding season. However, recent observations with the Lusitanian toadfish Halobatrachus didactylus (Batrachoididae) indicate that the emission of boatwhistles is not restricted to this period, which suggests a function in other behavioral contexts such as agonistic territorial interactions. We experimentally manipulated the social context of toadfish males to investigate whether boatwhistles are produced during territorial defense, by introducing ‘intruders’ in an experimental tank containing nesting ‘resident’ males. Furthermore, we examined whether parental care (eggs in the nest) affected the behavioral responses of resident males during territorial defense. Resident males defended their shelters producing sounds, mostly boatwhistles, towards intruders. Parental males revealed higher aggression levels, exhibiting additional threatening and attack behaviors. Boatwhistles registered during agonistic events were compared with the mate advertising boatwhistles recorded from small aggregations of nesting males in a natural breeding intertidal area. Agonistic boatwhistles were produced in lower and variable calling rates comparing with the advertising ones that were typically emitted in long series of calls. Agonistic boatwhistles were similar in duration and frequency harmonic structure (with a middle tonal phase) to the advertising calls, but presented less amplitude modulation, and lower dominant and fundamental frequencies. These acoustic differences were probably related to differences in calling rates and broadcast demands associated to the distance to the intended receiver. We provide first evidence that, apart from attracting mates, the toadfish boatwhistles also function as active ‘keep‐out’ signals during territorial defense.     

Identification and characterization of the intracellular poly-3-hydroxybutyrate depolymerase enzyme PhaZ of Sinorhizobium meliloti

Background  

S. meliloti forms indeterminate nodules on the roots of its host plant alfalfa (Medicago sativa). Bacteroids of indeterminate nodules are terminally differentiated and, unlike their non-terminally differentiated counterparts in determinate nodules, do not accumulate large quantities of Poly-3-hydroxybutyrate (PHB) during symbiosis. PhaZ is in intracellular PHB depolymerase; it represents the first enzyme in the degradative arm of the PHB cycle in S. meliloti and is the only enzyme in this half of the PHB cycle that remains uncharacterized.     

Gene expression and activity of urea cycle enzymes of rat hepatocytes cold stored up to 120h in University of Wisconsin solution

Urea cycle (UC) is the main pathway of ammonium removal. A deficiency in any of the five classical enzymes of the pathway causes a urea cycle disorder. Hepatocellular transplantation is one of the techniques applicable to treat this disorder. In the present work, we investigated the activities and the relative expression levels of two of the UC enzymes: Carbamyl phosphate synthetase I (CPSI) and ornithine transcarbamylase (OTC), in isolated hepatocytes preserved up to 120 h in University of Wisconsin (UW) solution at 0 degrees C, and during the rewarming of these suspensions. During preservation, CPSI showed differences in mRNA levels respect to time 0, while ornithine transcarbamylase remained unchanged. At the end of the rewarming, CPSI showed values of enzymatic activity and relative mRNA level comparable with the control, meanwhile, there was an increment in OTC activity. In line with these results, we found that hepatocytes cold preserved up to 120h in UW solution maintained their ability to remove an ammonium load comparable to freshly isolated hepatocytes. These data indicated that our preservation conditions up to 120h in UW solution followed by rewarming, preserves UC enzymes at levels similar to freshly isolated hepatocytes, allowing the use of these cells in bioartificial liver devices or hepatocellular transplantation.     

Correction: deviation of eyes and head in acute cerebral stroke

This is a correction article