Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant characters related to slug feeding: a re‐analysis of feeding studies using trait data from botanical databases and literature

Slugs feed on some plant species but not on others for reasons that are not yet fully understood. We re-examined the two largest studies on the preference of Arion lusitanicus for different plant species. Briner & Frank (1998) measured the consumption index of slugs (CIB) based on the dry leaf mass eaten per day per gram of slug mass. Kozlowski & Kozlowska (2009) also measured a consumption index of slugs (CIK) but on the basis of the area eaten per day per gram of slug mass. The two indices showed a moderate positive rank correlation. Briner & Frank (1998) found that slugs preferred annual to perennial plants and crops rather than wild species. On the other hand, Kozlowski & Kozlowska (2009) found no statistically significant difference in slug preference for annuals, biennials or perennials. Using botanical databases we selected plant traits related to slug herbivory and analysed 141 species. We first analysed the two data sets separately and found that CIB was higher for seedlings with a higher relative growth rate although this result was only marginally statistically significant. In addition, we found that annuals were consumed more than perennials and that cultivated plants were consumed more than wild plants. This is in agreement with the conclusions of Briner & Frank (1998). For CIK slugs consumed less from plants with high dry matter content (DMC). The use of classification and regression tree models solves the problem of analysing datasets with missing values. Regarding CIB, the tree models indicated that life cycle was the major branch. Within perennials, cultivated/wild origin of plants was the most important predictor of slug feeding. Within wild perennials slugs ate more from plants with low specific leaf area (SLA), i.e. relatively thick leaves. Within annuals we found the unexpected result that slugs ate more from plant species with either alkaloids or glucosinolates than from species without one of these compounds. For CIK, the results of tree models showed that slugs preferred shade-intolerant plants to shade-tolerant plant species. Within the shade-tolerant group slugs fed more on leaves with low DMC. We only partially understand which factors make plants acceptable to slugs. We discuss this issue along with the pros and cons of the two methods used to calculate CI.
Effect of Starter Cultures on Biogenic Amine Formation during Fermented Sausage Production.

Changes in biogenic amines, pH, water activity values. and counts of aerobic, lactic acid, Enterobacteriaceae , and pseudomonad bacteria were followed during production of dry sausage. The effect of two starter cultures, Lactobacillus plantarum plus Micrococcus carnosus and Pediococcus pentosaceus plus Micrococcus carnosus , on amine production was investigated. Raw materials used in sausage production only contributed spermine and spermidine to the final products. Tyramine, putrescine, and cadaverine contents increased during the fermentation stage, and tyramine was the prevailing amine in the final sausages. Sausages produced by fermentation with starters, as compared to natural fermentation (control), had a lower amount of tyramine, putrescine, and cadaver-ine' but differences in microbial counts were minor. Levels of spermine decreased during sausage production and those of spermidine remained relatively constant. Aerobic plate and lactic acid bacteria counts increased during ripening while levels of species of Enterobacteriaceae and pseudomonads decreased. Starters seemed to decrease the biogenic amine formation but did not prevent it. The high background flora naturally present on the starting meat and pork lard seemed to have a strong influence on biogenic amine formation during ripening.
Ethnic Segregation in the Netherlands: New Patterns, New Policies?

An impressive set of welfare state arrangements has kept ethnic segregation and concentration in Dutch cities to a relatively low level. Indices of segregation have also been relatively stable over the last two decades. This does not mean, however, that concentrations of ethnic minority groups are stable. Some types of neighbourhoods seem to have become less important as housing areas for ethnic minority groups, while others are becoming their main housing areas, especially for Turks and Moroccans. While in some cities this shifting pattern has already been characteristic for more than a decade, in other cities it is of more recent origin. We describe these shifting patterns of ethnic minority groups in the largest cities in the Netherlands (Amsterdam, Rotterdam, The Hague and Utrecht). We then focus on the policy response to these patterns and we briefly evaluate this response. Our main conclusion is that ethnic concentrations are not problematic in themselves, but that policy can significantly enhance the situation of (the inhabitants of) specific neighbourhoods. Copyright Royal Dutch Geographical Society 2002.
Sympathy for the devil: captive-management style did not influence survival, body-mass change or diet of Tasmanian devils 1 year after wild release

Abstract Context. The value of captive breeding for recovery programs of endangered carnivorous mammals is often questioned because of low post-release survival reported for founder animals following translocation. Aims. The aim of the present study was to test the effect of rearing method on survival and body mass of captive-raised Tasmanian devils (Sarcophilus harrisii) following release on an offshore island. We also compared the post-release diet of these devils with the diet of wild devils on mainland Tasmania, where a similar array of diet items is available. Methods. Twenty-eight captive-raised devils were released onto the island; 19 had been raised in intensive captive-management facilities (IC) and nine in free-range (22 ha) enclosures (FRE). Survival and body-mass change were compared between IC and FRE for up to 440 days post-release. Devil diet was assessed via scat analysis. Key results. A high proportion (96%) of the founders survived 1 year post-release. Pre-release captive-rearing method had no effect. Released devils gained an average of 14% of their original body mass, irrespective of captive-rearing method. There was very little difference in the diet of captive-reared devils released onto Maria Island relative to wild mainland devils: Tasmanian pademelon, Thylogale billardierii, was the primary food item for both. Conclusions. The intensity of captive rearing did not affect the survival of devils released onto Maria Island. This suggests that even devils held in IC facilities retain the innate behaviour required to scavenge and hunt prey, and therefore maintain bodyweight post-release. The lack of any threatening processes on the island is also likely to have contributed to the high survival rate 2 years post-release. Implications. Our study provided preliminary evidence that the release of captive-raised Tasmanian devils onto off-shore islands is a viable conservation action. Captive-breeding programs and captive-raised founders can play a viable and valuable role in the conservation action plans for recovery programs of endangered carnivorous mammals.
Populations of Escherichia coli in clinical samples of Urinary Tract Infections and bacteraemia

Extraintestinal pathogenic E. coli (ExPEC) strains are the main etiologic agent of urinary tract infections (UTIs). ExPEC strains are also reported to be the most common cause of bacteraemia in the world, which often originate from UTI. The population structure of UTI E. coli strains is well described in the literature with increased prevalence of multidrug resistance driven by extended spectrum β lactamases (ESBLs). ESBL carriage and multidrug resistance of bacteraemia E. coli is on the increase yet little information is available about their population structure. With the aim to define the bacteraemia population structure, E. coli isolated from urine samples and blood cultures were collected from the Nottingham University Hospital NHS trust over a five month period. Isolates were tested for antimicrobial resistance, ESBL and virulence associated gene (VAG) carriage, and were typed by MLST. Significantly higher ESBL driven multidrug resistant strains were observed in the bacteraemia E. coli compared to the UTI isolates with no significant difference in the carriage of VAGs. Our data shows a reduction in population diversity within the bacteraemia isolates compared to the concomitant urine sample population resulting in a small number of dominant sequence types (STs) (ST131, ST73, ST95) which is associated with ESBL conferred multi drug resistance and not specific virulence genes. This suggests that the increased prevalence of ESBL carriage in ExPEC isolates is leading to a selective advantage in a small number of dominant lineages causing bacteraemia in patients. Comparative genome analysis of selected isolates belonging to the dominant ST (ST73) from bacteraemia and UTI was performed to investigate the presence of bacteraemia specific loci that may explain the loss of diversity in bacteraemia. No genomic regions were identified specific for the bacteraemia ST73 isolates other than ESBL carriage. Plasmid profiling of the ESBL positive isolates of this ST73 group from bacteraemia and UTI identified diverse types of plasmids spread between the strains. No specific genomic loci were identified specific for ESBL positive ST73 isolates from bacteraemia and UTI. This concludes that random acquisition of ESBL plasmids by any ST73 E. coli may select for its progression to bacteraemia which is serious and debilitating. Our study provided a comprehensive snapshot of the E.coli population structure from contemporaneous clinical cases of UTI and bacteraemia. The large increase in multi-drug resistance in bacteraemia ExPEC populations compared to co-circulating UTI populations is of clinical concern and represents a challenge in control and treatment of serious extra-intestinal E. coli infections. This provides an important clinical insight into how common E. coli STs could adapt to become dominant bacteraemia agents.
Plant functional groups within a tropical forest exhibit different wood functional anatomy

Summary Understanding the anatomical basis of plant water transport in forest ecosystems is crucial for contextualizing community-level adaptations to drought, especially in life-form-rich tropical forests. To provide this context, we explored wood functional anatomy traits related to plant hydraulic architecture across different plant functional groups in a lowland tropical rain forest. We measured wood traits in 90 species from six functional groups (mature-phase, understorey and pioneer trees; understorey and pioneer shrubs; vines) and related these traits to intrinsic water-use efficiency (WUEi) as a measure of physiological performance. We also examined vessel size distribution patterns across groups to determine trade-offs in theoretical hydraulic safety vs. efficiency. Some plant functional groups exhibited significant differences in vessel parameters and WUEi. Vessel diameters in vines and pioneer trees were two- to threefold greater on average than in understorey trees and shrubs. Contrastingly, vessels in understorey trees and shrubs fell within the smaller size classes, suggesting greater safety mechanisms. In addition to these trends, large vessel dimensions were important predictors of WUEi among the functional groups. We conclude that wood functional anatomy profiles varied across plant functional groups in a tropical rain forest. These groups can therefore serve as a framework for further investigations on structure–function relationships and a sound basis for modelling species responses to drought. A lay summary is available for this article.
Gastric protective effect of Lentinus edodes against ethanol-induced ulceration

The extract of L. edodes dose dependently (75-300 mg/kg) inhibited ethanol-induced gastric lesions in rats. Both local and systemic protective effects of the extract were observed which may be related to its inhibition of gastric motility and stimulation of formation of endogenous prostaglandins. Gastric mucus content was not affected by the extract.
Overcoming missing data in phylogenetic analysis of shotgun sequencing to detect HIV adaptation to immune response

DNA sequencing gives us insight into how viruses adapt to their host immune systems. Studies of viral populations typically employ deep amplicon sequencing with next-generation reads to capture a detailed sample of genetic variation in a population. The high amount of overlapping sites in a multiple sequence alignment of reads from amplicon sequencing form ideal input for phylogenetic reconstruction, a necessary step for studying evolutionary relations in a population. However, the typical short read lengths of <600 bp from next generation sequencing technology with the best sequence error rate impose a severe limit on the width of genomic regions for which evolutionary relationships can be analyzed. Shotgun sequencing, in which DNA is fragmented at random positions, is an efficient alternative to amplicon sequencing for covering wider regions of a genome with sufficient depth. Due to the random staggered positions of shotgun reads in a genome, an extremely high percentage of missing data can result in multiple sequence alignment of shotgun sequencing. The absence of sequence homology across the entire set of short reads makes it impossible to reconstruct a phylogenetic tree, limiting the utility of shotgun data for phylogenetic analysis. We developed the Umberjack software pipeline, which employs the ‘sliding window’ approach to minimize the effect of missing data during phylogenetic reconstruction and obtain evolutionary statistics to detect sites under selection. Using Umberjack to measure a new metric of directional selection I, significant directional selection was detected in treatment-naive HIV populations at sites with previously documented associations with cytotoxic T-lymphocyte (CTL) response. Further, substitutions towards wild-type amino acids were found to occur early within the population’s history, but rarely occurred at a site after the appear-
Patterns of variation in forst-year seedling traits within and among Douglas-fir breeding zones in Southwest Oregon

(.) Patterns of variation among breeding zones were strongly associated with location variables (distance from the ocean, latitude, and elevation) and seemed to reflect adaptation to moisture and temperature gradients in the region. Families from the drier, southern-inland zones had heavier seeds and produced seedlings that grew slower and had earlier budset, less frost damage, and more second flushing than families from breeding zones with cooler, moister climates. Elevation clines were most evident for traits related to phenology; seedlings from higher elevation breeding zones had earliest budset and least frost damage. (.)
Allochrusa lutea (Caryophylloideae, Caryophyllaceae) a new species from Iran

Allochrusa lutea sp. nov. is here described and illustrated from the Zanjan Province, NW of Iran. A comparison with other Allochrusa species is presented. The more similar species is A. persica from which A. lutea differ by shape of ovary and number of ovules, petals color and the ratio of inflorescence length to stem length. A. lutea is to be considered as endemic to the northern-west of Iran.
Martens in a novel habitat – The importance of prey and habitat structure

The Pacific marten (Martes caurina) is thought to be a forest specialist closely linked to older forests with high canopy cover and dense shrubs. It is therefore highly surprising that a small population have been found in the coastal sand dunes in Oregon, United States. The martens seem to be choosing this habitat even though large areas of older forests are available just next to the dunes. With this project we wanted to explore potential reasons why the marten seem to prefer this unique habitat. Martens are small slender-bodied carnivores with high metabolic rates which means they need to eat continuously. On a daily basis a marten must consume approximately 25% of its own body weight which equates to for example seven voles and a considerable hunting effort. We predicted that there would be more prey on the dunes compared to the older forest which could explain this unusual marten habitat use. However, martens are also threatened by other predators both by potential competitors such as foxes and skunks that hunt the same prey, and by larger carnivores that prey on martens such as bobcats and owls. We therefore also wanted to investigate whether the martens were avoiding the older forest because there are more carnivores there. We used camera traps (cameras triggered by movement) to assess the abundance of small mammals and birds as well as presence of martens and other carnivores in Siuslaw National Forest, Oregon. We also recorded information on the vegetation such as shrub cover, canopy cover and tree height to describe the habitat structure. As predicted, the relative abundance and diversity of prey species was higher in the dune forest compared to the interior forest. The presence of competitors and predators were often equal or higher within the dunes which suggests that competition with other predators is not influencing the habitat selection of the martens. The shrub cover was higher in the dunes while the canopy cover was higher in the interior forest. There may be several reasons why there are more prey species in the dune forest, such as a high abundance of food resources like mushrooms and berries. It could also be the high shrub cover which provides cover from predators. Similarly, the martens may also prefer the dune forest because they are more protected from predators there, but also because there are more prey available. Our study suggests that martens are more flexible in their habitat use than previously believed, and that relative abundance of prey and a high shrub cover may be more important than forest age. These findings are important for management of the dune forest and for conservation of the rare coastal marten. Advisor: Dr Taal Levi (OSU) and Dr Katie Moriarty (U.S Forest Service) Master´s Degree Project 60 credits in Conservation Biology 2015-2016 Department of Biology, Lund University (Less)
Cellulase-free Xylanase: Production by Thermomyces lanuginosus TISTR3465 in solid state fermentation and efficiency on bioleaching

The mixed substrate (12g) consisting of NaOH-treated corncob, wheat bran and rice husk at ratios between 5:5:2 to 4:6:2 were optimal ratios for xylanase production 250 ml Erlemeyer flask by Thermomyces lanuginosus TISTR3465 in static solid state cultivation at 70% initial moisture content at 50 ◦C. Addition of 0.12-0.75 g wood xylan to the substrates enhanced the enzyme production 1.30-1.58 folds. Addition of nitrogen sources to the mixed substrates did not increase the enzyme production indicating that wheat bran served as a sufficient nitrogen source. A temperature of 45-50 ◦C with 70% initial moisture content of the mixed substrates was the optimal conditions for the enzyme production by this strain. Aeration in a static tray solid-state culture was remarkably required for the enzyme production by this strain at higher thickness of substrate beds. Maximum xylanase activity, 1764 U/g dry solid, was obtained at a substrate thickness of 1 cm with an aeration rate of 0.24 l/g/h after cultivation for 5 days. The xylanase from T. lanuginosus TISTR3465 was found to be effective in release of reducing sugars from eucalyptus pulp. Treatment of pulp with -xylanase (220 U/g dry weight pulp) followed with 2% hydrogen peroxide significantly decreased in kappa number (5.7 U) and improved brightness up to 45.2%
SURVEY AND SUMMARY H1 histones: current perspectives and challenges

H1 and related linker histones are important both for maintenance of higher-order chromatin structure and for the regulation of gene expression. The biology of the linker histones is complex, as they are evolutionarily variable, exist in multiple isoforms and undergo a large variety of posttranslational modifications in their long, unstructured, NH2 -a nd COOH-terminal tails. We review recent progress in understanding the structure, genetics and posttranslational modifications of linker histones, with an emphasis on the dynamic interactions of these proteins with DNA and transcriptional regulators. We also discuss various experimental challenges to the study of H1 and related proteins, including limitations of immunological reagents and practical difficulties in the analysis of posttranslational modifications by mass spectrometry.
Processing of different sensory qualities in the olfactory bulb of Xenopus laevis studied by advanced line illumination microscopy

The olfactory system is renowned for its ability to sample and process a tremendously large odorant space. Lately, it has been shown that other sensory qualities such as temperature and pressure are detected in the olfactory system. However, little is known about how they are processed within the olfactory bulb and how this multisensory information is integrated in the context of olfaction. In this thesis, two specific olfactory glomeruli — the mechanosensitive beta- and the thermosensitive gamma -glomerulus — in the olfactory bulb of Xenopus laevis tadpoles were analyzed by means of a custom-built line illumination microscope. The line illumination technique was combined with subtraction imaging and pixel reassignment to perform fast calcium recordings in three dimensions. These recordings, covering first- and second-order neurons in the olfactory bulb, revealed a strong interconnection of both sensitivity to temperature drops as well as mechanosensitivity with olfaction. Dual-sensitive mitral/tufted cells responding to amino acids as well as to temperature drops were located in the proximity of the -glomerulus. A dose-response curve for the mechanosensitivity of the beta-glomerulus was measured. Additionally, the same glomerulus showed sensitivity to a surprisingly broad spectrum of single amino acids, thereby combining mechano- and chemosensitivity in the same structure. The axon separation of different olfactory receptor neurons within a single glomerulus was successful using double staining electroporation. Recordings obtained from such stainings suggest that the sensitivity of the beta-glomerulus to amino acids was caused by a single broadly tuned olfactory receptor. Lastly, a sufficient resolution for single axon as well as for single dendrite recordings within the beta-glomerulus was achieved by line illumination microscopy. The demonstrated increase in efficiency of the line scanning technique enables future experiments with two calcium indicators to analyze the signal transmission within a single glomerulus.