PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on α- and β-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3–V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in β-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based α- and β-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions

Drought tolerance phenotyping using thermal imaging : high throughput phenotyping of Pinus sylvestris

Climate change is an emerging problem in the world. One of the many challenges that comes with it is an increase of droughts. Droughts cause stress for plants, which impact the growth. An important stage for trees is the seedling stage, and an important tree in the forest is the Scots pine (Pinus Sylvestris), therefore this study will focus on these. High throughput phenotyping is a tool that can help identifying drought tolerance. In this paper the use of thermal imaging as a way to achieve high throughput phenotyping in Pinus sylvestris for transpiration and its links to drought tolerance was evaluated. Another possible phenotyping method, used in this study, is if drought tolerance can be evaluated by their divergence from an average growth. Experiment took place during the summer of 2022 and plants evaluated started growing that same year. It took place inside a greenhouse and with a drought/control treatment. The results revealed differences between natural and bred plant material, and also between northern and southern plant material. With bred and southern plants expressing lower stress compared to the others. A strong negative association between total volume and canopy temperature for drought treated plants suggest there is potential for using infrared light to evaluate drought tolerance. Also consistent patterns between the transpiration and divergence from average growth supports the idea that thermal imaging could be used for high throughput phenotyping

Phenotypic variation for BOAS within four brachycephalic dog breeds

Brachycephalic obstructive airway syndrome (BOAS) is an upper airway obstruction that was considered the most severe disorder identified according to the Generic Illness Severity Index for Dogs. The aim of this master thesis was to investigate the phenotypic variance correlated to BOAS in the Swedish population of four brachycephalic breeds; English Bulldog, French Bulldog, Pug and Boston Terrier and discuss their welfare implications. The project consisted of two parts; one inventory and one survey. The inventory consists of conformational description of the four brachycephalic breeds and the survey was to investigate the BOAS related problems in the same breeds and their owner’s perspective of health and welfare. The conformational risk factors correlated to BOAS found in this study were snout length and craniofacial ratio for French Bulldogs, snout length, chest girth, neck length, sternum length and craniofacial ratio for English Bulldogs and none for either Pugs or Boston Terriers. According to the survey noisy breathing and heat intolerance were the most common BOAS-related problems for all the four breeds in this study. The conclusion of the study was that there was enough phenotypic variance to improve the BOAS problem for both French Bulldogs and English Bulldogs. For Boston Terriers the BOAS problem was not severe enough in this study to get a result and for the Pugs the phenotypic variance is too small. For the welfare aspect this study showed that BOAS is a welfare problem and that there was a normalization for some of the problems connected to BOAS for English Bulldogs, French Bulldogs and Pugs

Human motor control, autonomic and decision processes under physical and psychological stress. Instinctive, reflexive and adaptive aspects.

The stress response is governed by automatic neurological and hormonal processes that occur before we become consciously aware of a dangerous situation. If stress ensues for 15-30 seconds, the hormonal processes may have progressed so far that recovery takes an hour or longer instead of minutes. Stress can affect our behavior and in certain professions, such as the police force and emergency services, being in stressful situations is routine. When the stress imparted on an action is low, there may be little detriment to performance. However, when the stress imparted on an action is high, performance may be reduced and viewed as unsatisfactory. This thesis has examined the situational characteristics and performance of police officers in stressful incidents where firearms and pepper spray have been used, and during training scenarios designed to induce stress. Pepper spray and firearms were often used differently in real situations, both operationally and technically, compared to the way they were used during training. When armed assailants were encountered in actual incidents, weapons were often used late on and at very short ranges. One real life event studied in detail showed that both police officers and civilian witnesses suffer from similar perceptual and memory distortions. When mimicking real situations for training through simulations, stress levels increased as evidenced by an increase in heart rate which may be used to ensure the closeness of training simulations to real events. When assessing the suitability of pupil dilation as a stress measure, the pupil underwent dilation in spite of large illumination increases, and the pupils also dilated when a threat emerged early in stress-inducing scenarios. Subjective assessments made by six experts separately, rated performance as being impaired in the simulated stress training in addition to poorer performance of a highly trained, complex, motor skill. To conclude, stress can affect police officers during interventions and training, as it impaired perception and memory, cognition, decision-making and the motor skills necessary for equipment and weapon use. Hence, the consequences of stress responses should be considered when designing tactics, training and equipment so that tasks can be carried out well when stress is heightened. An increased understanding of physiological and behavioral changes to stressful situations in police officers will contribute to rationalizing outcomes and influencing policy based on scientific empirical and physiological grounds

Fluorescently labeled prey surrogates in combination with fluorescence-activated cell sorting successfully discriminate actively feeding mixotrophs in a lake water sample

Mixotrophic protists are capable of acting both as primary producers and primary consumers at the base of the aquatic food web, thus constituting key organisms in ecosystems where they are abundant. However, their identity, abundance, ecological dynamics, and biogeochemical impact in aquatic ecosystems remain understudied in comparison to classically demarcated autotrophs or heterotrophs. In this study, we make use of fluorescently labeled prey and fluorescence-activated cell sorting to taxonomically identify actively-feeding individual mixotrophic flagellates from lake water. Replicated experiments were carried out to assess the performance of three different fluorescently labeled prey types and a fluorescent dye targeting food vacuoles. In the experiments, water from an oligotrophic lake was exposed independently to each type of reporter and cells were individually sorted based on fluorescent signals for predation and chlorophyll a. A total of 927 individual single cells were successfully recovered, with all fluorescent reporters exhibiting high sensitivity for putative mixotrophic taxa: overall, 87% of the occurrences could be assigned to dictyochophytes, 9% to chrysophytes, and 3% to dinoflagellates. As a result, we were able to detect cryptic diversity within pedinellid algae and report a Prorocentrum-like freshwater occurrence. We argue that this procedure can be a valuable tool to uncover relevant and unexpected active mixotrophic species in a wider range of aquatic environments, and could easily be coupled to other techniques to describe the finer details of the trophic status of aquatic microbial communities

Feeding Mixed Grass-Clover Silages with Elevated Sugar Contents to Dairy Cows

Grasses with high sugar content (WSC) have been claimed to increase feed intake and milk production and at the same time give more efficient N utilisation and thus reduce pollution (e.g. Miller et al., 2001). In an ongoing EU-supported project (“Sweetgrass”), we have grown the new varieties of perennial ryegrasses and fed them to dairy cows. Results from the first year’s experiment when pure ryegrass silages made from standard or high-sugar varieties were fed, showed small differences in feed intake, milk production and N partitioning. In order to test the principle, it was therefore decided to increase the difference in sugar content in the following experiment by mixing sucrose into the silage before feeding

Det gröna torget

Urbana miljöers utbredning har haft stor påverkan på den naturliga miljön och många djur och insektsarters naturliga habitat har försvunnit och ersatts av hårdgjord markyta och byggnader. Detta har inte bara påverkat djur och insektsvärlden utan även oss människor negativt i form av förorenad luft, översvämningar och störande buller från fordon. I det här arbetet utförs en litteraturstudie kring ämnet biodiversitet och hur man kan stärka det på urbana miljöer. Bland annat samlas information om vilka växter som lockar till sig djur och hur man skapar habitat för dessa in för att ta reda på hur man får djur att trivas. Torg har valts ut som fokus för studien eftersom det anses vara det mest klassiska urbana centret enligt många stadsplanerare och har oftast bestått av tomma öppna ytor som ska kunna hantera stora mängder människor och aktiviteter i form av exempelvis samlingar, spring och återhämtning på utplacerade stolar och bord. Det torg som valts ut för studien är S:t Knuts torg i Malmö stad. Efter litteraturstudien genomförs platsobservationer av fyra torg i Malmö med fokus på användandet av växtmaterial; Nobeltorget, Gustav Adolfs torg, Stortorget och Lilla torg. Därefter jämförs dessa för att få en djupare förståelse för hur man kan tänka vid design av torg. Sedan genomförs en platsobservation även på S:t Knuts torg där platsens möjliga potential och brister tas upp och diskuteras. Slutligen genomförs baserat på den information som samlats in en omdesign av S:t Knuts torg där fokus ligger på biodiversitet och en stor mängd växtmaterial placeras på platsen men på ett vis som ska tillåta att torget förblir just ett torg och människor kan använda torget som ett torg.The urbanization has had a great affect on the natural environment and many animal and insect species natural habitats have disappeared and been replaced by hard surfaces and buildings. This has not only affected the world of animals and insects but also us humans negatively in the form of air pollution, floods and obtrusive noise from vehicles. In this study a literature review has been performed in order to gather information about the subject biodiversity and how to increase it in urban environments. Among other things information about which plants attracted insects and animals and how to create habitat for these creatures and make them thrive. Squares have been chosen for focus for this since they are considered by many city planners to be the most classical urban center and often consists of an open empty space made to be able to handle a great amounts of people and activities such as gatherings, running around and recreational activities on laid out tables and chairs. The square chosen for this study is S:t Knuts square in Malmö city. After the literature review a on-site observation on the following squares in Malmö with a focus on the use of planting material; Nobeltoret, Gustav Adolfs torg, Stortorget and Lilla Torg. Thereafter these squares are compared to gain a deeper understanding of how to think when designing squares. Afterwards a similar observation is done on S:t Knuts Square and its potentials and flaws are discussed. Finally based on the information gathered in the previous steps are considered and a redesign of S:t Knuts square is created. The new design will be focused on an increased biodiversity while still allow the square to remain a square and allow people to use the square as a square