Effect of Periodic Oscillations of Artificial Light Emission on Photosynthetic Activity

The effects of periodic oscillation of artificial light and of the frequency of these oscillations on photosynthetic assimilation has been measured. When the frequency is sufficiently high, the gross CO₂ assimilation in fluctuating light is identical to the assimilation of the leaf under a continuous illumination equal to the efficient intensity of the intermittent light. It is necessary to consider the quality of the sensor used for measuring light intensity, particularly its response velocity.     

Effects of habitat fragmentation on the timing of Crested Tit Parus cristatus natal dispersal

Crested Tit Parus cristatus young from first broods dispersed 1 week later if they were born in small isolated pine plots ('habitat fragments') compared with individuals in a large pine forest ('continuous habitat'). This delay in dispersal was caused by an extended period between fledging and dispersal. In second broods, the delay was even longer due to the interbrood interval being 9 days longer in habitat fragments. As nestlings in habitat fragments had a lower body-mass, and age at dispersal was negatively correlated with nestling body-mass within each nest, the postponed dispersal from fragments might be explained partly by a lower body-mass. Alternatively, postponed dispersal from fragments could result from a barrier effect caused by reluctance to cross inhospitable habitat.
Immigration by young from first broods into habitat fragments was delayed by approximately 3 weeks, and proportionally more second brood emigrants were recovered in this type of habitat. These results are in agreement with the hypothesis that fragments are second-choice habitat. Early immigrants into continuous habitat had a higher probability of settlement in winter flocks compared with late ones, independent of condition or age. Therefore, Crested Tits born in habitat fragments probably have a lower chance of settling in first-choice habitat.     

Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

The evolution of phylogeographic data sets

Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next‐generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic data sets over the past 20 years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled and the total number of single nucleotide polymorphisms (SNPs) per data set has improved over time, with particularly dramatic increases within the past 5 years. Interestingly, uniparentally inherited organellar markers (e.g. animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single‐species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicates that the median number of SNPs per data set for studies published by the end of the year 2016 may approach ~20 000. This survey provides baseline information for understanding the evolution of phylogeographic data sets and underscores the fact that development of analytical methods for handling very large genetic data sets will be critical for facilitating growth of the field.     

Sulphur stable isotopes can distinguish trophic dependence on sediments and plankton in boreal lakes

1. Stable isotopes of carbon are useful for differentiating between freshwater food chains based on planktonic algae or benthic algae, but are reported to be of limited use for identifying food chains based on sedimentary detritus. Because data from marine systems suggest that stable isotopes of sulphur (δ³⁴S values) have potential in this regard, we tested their utility in freshwater lakes.
2. We found that sulphate in the water column of four boreal lakes was enriched in ³⁴S compared to the sulphur in bulk sediments from these lakes. Furthermore, within a given lake, insects known to feed on sediment (directly or via predation) had δ³⁴S values similar to those of sediment, whereas planktonic and benthic invertebrates known to feed on suspended particles had δ³⁴S values similar to those of sulphate in the water column.
3. Using the stable S isotope values of invertebrates that obtain their S from either the sediment or the water column as end members in a two-source mixing model, we show that two fish species obtain their food from both planktonic and sedimentary sources. Furthermore, model results suggest that, as expected, the more benthic-feeding fish species obtains more of its S from the sediment compartment than does the species that feeds in the water-column.
4. Our results suggest that measurements of stable sulphur isotopes provide a means of distinguishing between members of food chains that are based in the water column from those based on sedimentary detritus. As such, they would be a useful complement to stable C isotopes that are used to distinguish between food chains based on planktonic or benthic algae.     

COMPARISON OF THE EFFECT OF DIFFERENT SHORT CHAIN FATTY ACIDS ON THE GROWTH AND DIFFERENTIATION OF HUMAN COLONIC CARCINOMA CELL LINESIN VITRO

The aim of this study was to compare the effects of acetate, propionate, butyrate, iso-butyrate, valerate, iso-valerate and caproate on cell growth and on the activities of alkaline phosphatase (AP) and dipeptidyl aminopeptidase IV (DPP IV) by three human colonic adenocarcinoma cell lines. In addition to butyrate, propionate and valerate inhibited cell proliferation of the three cell lines. The other SCFAs did not influence cell proliferation. AP and DPP IV activities were strongly stimulated by butyrate on two of the three cell lines. On HT-29, AP was strongly stimulated, however DPPIV expression remained undetectable. Propionate and valerate exhibited a weaker stimulation, the other SCFAs being ineffective. The effect of SCFAs on cell proliferation and differentiation clearly depends on the number of carbons and on the configuration of the basic structure of the molecule.     

Heterologous expression of bacteriocin E-760 in Chlamydomonas reinhardtii and functional analysis

The use of antimicrobial peptides (AMPs) synthesized by bacteria (bacteriocins) is an alternative for combating multidrug resistant bacterial strains and their production by recombinant route is a viable option for their mass production. The bacteriocin E-760 isolated from the genus Enterococcus sp. has been shown to possess inhibitory activity against Gram-negative and Gram-positive bacteria. In this study, the expression of a chimeric protein coding for E-760 in the nucleus of C. reinhardtii was evaluated, as well as, its antibacterial activity. The synthetic gene E-760S was inserted into the genome of C. reinhardtii using Agrobacterium tumefaciens. A transgenic line was identified in TAP medium with hygromycin and also by PCR. The increment in the culture medium temperature of the transgenic strain at 35 °C for 10 minutes, increased the production level of the recombinant protein from 0.14 (Noninduced culture, NIC) to 0.36% (Induced culture, IC) of total soluble proteins (TSP); this was quantified by an ELISA assay. Recombinant E-760 possesses activity against Staphylococcus aureus in 0.34 U log, Streptococcus agalactiae in 0.48 U log, Enterococcus faecium in 0.36 U log, Pseudomonas aeruginosa in 2 U log and for Klebsiella pneumoniae, the activity was 0.07 U log. These results demonstrate that the nucleus transformation of C. reinhardtii can function as a stable expression platform for the production of the synthetic gene E-760 and it can potentially be used as an antibacterial agent.     

Influence of host phylogeographic patterns and incomplete lineage sorting on within-species genetic variability in Wigglesworthia species, obligate symbionts of tsetse flies

Vertical transmission of obligate symbionts generates a predictable evolutionary history of symbionts that reflects that of their hosts. In insects, evolutionary associations between symbionts and their hosts have been investigated primarily among species, leaving population-level processes largely unknown. In this study, we investigated the tsetse (Diptera: Glossinidae) bacterial symbiont, Wigglesworthia glossinidia, to determine whether observed codiversification of symbiont and tsetse host species extends to a single host species (Glossina fuscipes fuscipes) in Uganda. To explore symbiont genetic variation in G. f. fuscipes populations, we screened two variable loci (lon and lepA) from the Wigglesworthia glossinidia bacterium in the host species Glossina fuscipes fuscipes (W. g. fuscipes) and examined phylogeographic and demographic characteristics in multiple host populations. Symbiont genetic variation was apparent within and among populations. We identified two distinct symbiont lineages, in northern and southern Uganda. Incongruence length difference (ILD) tests indicated that the two lineages corresponded exactly to northern and southern G. f. fuscipes mitochondrial DNA (mtDNA) haplogroups (P = 1.0). Analysis of molecular variance (AMOVA) confirmed that most variation was partitioned between the northern and southern lineages defined by host mtDNA (85.44%). However, ILD tests rejected finer-scale congruence within the northern and southern populations (P = 0.009). This incongruence was potentially due to incomplete lineage sorting that resulted in novel combinations of symbiont genetic variants and host background. Identifying these novel combinations may have public health significance, since tsetse is the sole vector of sleeping sickness and Wigglesworthia is known to influence host vector competence. Thus, understanding the adaptive value of these host-symbiont combinations may afford opportunities to develop vector control methods.     

Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region

Background  

PPE38 (Rv 2352c) is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC) member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM). Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions.