Evaluation of commercial soy sauce <Emphasis Type="Italic">koji</Emphasis> strains of <Emphasis Type="Italic">Aspergillus oryzae</Emphasis> for γ-aminobutyric acid (GABA) production

In this study, four selected commercial strains of Aspergillus oryzae were collected from soy sauce koji. These A. oryzae strains designated as NSK, NSZ, NSJ and NST shared similar morphological characteristics with the reference strain (A. oryzae FRR 1675) which confirmed them as A. oryzae species. They were further evaluated for their ability to produce γ-aminobutyric acid (GABA) by cultivating the spore suspension in a broth medium containing 0.4 % (w/v) of glutamic acid as a substrate for GABA production. The results showed that these strains were capable of producing GABA; however, the concentrations differed significantly (P < 0.05) among themselves. Based on the A. oryzae strains, highest GABA concentration was obtained from NSK (194 mg/L) followed by NSZ (63 mg/L), NSJ (51.53 mg/L) and NST (31.66 mg/L). Therefore, A. oryzae NSK was characterized and the sequence was found to be similar to A. oryzae and A. flavus with 99 % similarity. The evolutionary distance (K _nuc) between sequences of identical fungal species was calculated and a phylogenetic tree prepared from the K _nuc data showed that the isolate belonged to the A. oryzae species. This finding may allow the development of GABA-rich ingredients using A. oryzae NSK as a starter culture for soy sauce production.     

Cross‐generational costs of compensatory growth in nine‐spined sticklebacks

Compensatory growth (CG) is a form of phenotypic plasticity allowing individuals’ growth trajectories to rebound after a period of resource limitation, but little is known about the reproductive and cross‐generational costs of CG. We studied the potential costs of CG by exposing female nine‐spined sticklebacks Pungitius pungitius to 1) high (favourable), 2) low (stressful), and 3) recovery (initially stressful, subsequently favourable) feeding treatments, and quantified the effects of these treatments on female reproductive traits (clutch, egg and yolk size), and on the size of their offspring. The low feeding treatment reduced female size relative to the high and recovery feeding treatments, which produced equally large females. Hence, females from the recovery treatment demonstrated CG and full growth compensation. Feeding treatments had significant effects on clutch, yolk, egg and larval size, also when the effect of female size was controlled for. However, these effects came about mostly because females from the low feeding treatment produced small clutches with large eggs (containing little yolk) and larvae, whereas females from the recovery feeding treatment produced as large clutches, eggs (with similar amounts of yolk) and larvae as females from the high feeding treatment. Yet, structural equation modelling revealed that while a direct effect of female size on offspring size was positive in the low and high feeding treatments, it was negative in the recovery feeding treatment, independently of egg and clutch size. This indicates a cross‐generational tradeoff between female and offspring sizes in the recovery feeding treatment. Also the tradeoff between clutch and larval size was more pronounced in recovery than in low or high feeding treatments. Hence, apart from demonstrating that environmental influences experienced by females during their development have the potential to influence their size, fecundity and reproductive traits, the results also provide evidence for complex cross‐generational costs of recovery growth.     

Fishes of the southeastern Brazil Atlantic Forest

The largest preserved areas of Atlantic Forest are located in the southeastern region of Brazil. Estuaries, mangroves, rivers and streams are home to a community of fish that is still poorly understood. The composition of fish species and their relationships with environmental conditions were used to identify homogeneous areas within a landscape of 33,000 km². A total of 6,542 specimens, representing 124 species and 13 orders of bony fishes were collected at 102 sampling stations. Resulting scores from a canonical correspondence analysis applied to biological and environmental data were used in a cluster analysis to identify fish species with similar spatial distributions and localities with similar fish fauna and abiotic conditions. Five micro-regions were identified, with homogeneous compositions of species, allowing better planning of conservation of aquatic biodiversity. Despite a high degree of preservation, impacts due to deforestation, drainage of wetlands and overfishing were detected, as well as the introduction of 41 exotic species.     

Fiddling in biodiversity hotspots while deserts burn? Collapse of the Sahara's megafauna

Biodiversity hotspots understandably attract considerable conservation attention. However, deserts are rarely viewed as conservation priority areas, due to their relatively low productivity, yet these systems are home to unique species, adapted to harsh and highly variable environments. While global attention has been focused on hotspots, the world's largest tropical desert, the Sahara, has suffered a catastrophic decline in megafauna. Of 14 large vertebrates that have historically occurred in the region, four are now extinct in the wild, including the iconic scimitar‐horned oryx (Oryx dammah). The majority has disappeared from more than 90% of their Saharan range, including addax (Addax nasomaculatus), dama gazelle (Nanger dama) and Saharan cheetah (Acinonyx jubatus hecki) – all now on the brink of extinction. Greater conservation support and scientific attention for the region might have helped to avert these catastrophic declines. The Sahara serves as an example of a wider historical neglect of deserts and the human communities who depend on them. The scientific community can make an important contribution to conservation in deserts by establishing baseline information on biodiversity and developing new approaches to sustainable management of desert species and ecosystems. Such approaches must accommodate mobility of both people and wildlife so that they can use resources most efficiently in the face of low and unpredictable rainfall. This is needed to enable governments to deliver on their commitments to halt further degradation of deserts and to improve their status for both biodiversity conservation and human well‐being. Only by so‐doing will deserts be able to support resilient ecosystems and communities that are best able to adapt to climate change.     

Scanning electron microscopic assessment on surface morphology of preserved human amniotic membrane after gamma sterilisation

Human amniotic membrane that has been processed and sterilised by gamma irradiation is widely used as a biological dressing in surgical applications. The morphological structure of human amniotic membrane was studied under scanning electron microscopy (SEM) to assess effects of gamma radiation on human amniotic membrane following different preservation methods. The amniotic membrane was preserved by either air drying or submerged in glycerol before gamma irradiated at 15, 25 and 35 kGy. Fresh human amniotic membrane, neither preserved nor irradiated was used as the control. The surface morphology of glycerol preserved amnion was found comparable to the fresh amniotic membrane. The cells of the glycerol preserved was beautifully arranged, homogonous in size and tended to round up. The cell structure in the air dried preserved amnion seemed to be flattened and dehydrated. The effects of dehydration on intercellular channels and the microvilli on the cell surface were clearly seen at higher magnifications (10,000×). SEM revealed that the changes of the cell morphology of the glycerol preserved amnion were visible at 35 kGy while the air dried already changed at 25 kGy. Glycerol preservation method is recommended for human amniotic membrane as the cell morphological structure is maintained and radiation doses lower than 25 kGy for sterilization did not affect the appearance of the preserved amnion.     

Prospects for fen meadow restoration on severely degraded fens

The majority of fens in Europe have been transformed for agricultural purposes and have disappeared or become degraded. Fen meadows that developed under low-intensity management of fens also have become degraded. In this paper, we consider the available restoration methods, biotic constraints for restoration and new prospects and approaches for the restoration of severely degraded fens. Due to irreversible changes in landscape settings, hydrology, soil and trophic conditions, a full restoration to natural mires is unlikely. Yet, an improvement of the ecosystem functions and revival of biodiversity in degraded fens is possible. A restoration of semi-natural meadows is one of the alternative targets. Important for restoration efforts to succeed are a sufficient reduction of nutrient levels and preventing acidification. In general, a combination of topsoil removal and seed transfer is an effective measure for fen meadow restoration, provided that groundwater seepage can be re-established. There are also several biotic limitations to fen meadow restoration, due to limited propagule availability of target species and the legacy of the former vegetation in form of its soil seed bank and high seed production by unwanted species. Under the present environmental conditions, the re-development of fen meadows on degraded fens will result in species compositions different from those observed in the past and such restoration may require considerable time and effort.     

Replication and recombination factors contributing to recombination-dependent bypass of DNA lesions by template switch

Damage tolerance mechanisms mediating damage-bypass and gap-filling are crucial for genome integrity. A major damage tolerance pathway involves recombination and is referred to as template switch. Template switch intermediates were visualized by 2D gel electrophoresis in the proximity of replication forks as X-shaped structures involving sister chromatid junctions. The homologous recombination factor Rad51 is required for the formation/stabilization of these intermediates, but its mode of action remains to be investigated. By using a combination of genetic and physical approaches, we show that the homologous recombination factors Rad55 and Rad57, but not Rad59, are required for the formation of template switch intermediates. The replication-proficient but recombination-defective rfa1-t11 mutant is normal in triggering a checkpoint response following DNA damage but is impaired in X-structure formation. The Exo1 nuclease also has stimulatory roles in this process. The checkpoint kinase, Rad53, is required for X-molecule formation and phosphorylates Rad55 robustly in response to DNA damage. Although Rad55 phosphorylation is thought to activate recombinational repair under conditions of genotoxic stress, we find that Rad55 phosphomutants do not affect the efficiency of X-molecule formation. We also examined the DNA polymerase implicated in the DNA synthesis step of template switch. Deficiencies in translesion synthesis polymerases do not affect X-molecule formation, whereas DNA polymerase δ, required also for bulk DNA synthesis, plays an important role. Our data indicate that a subset of homologous recombination factors, together with DNA polymerase δ, promote the formation of template switch intermediates that are then preferentially dissolved by the action of the Sgs1 helicase in association with the Top3 topoisomerase rather than resolved by Holliday Junction nucleases. Our results allow us to propose the choreography through which different players contribute to template switch in response to DNA damage and to distinguish this process from other recombination-mediated processes promoting DNA repair.