Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating ruminal nitrogen metabolism

Nitrogen losses from dairy production have negative impacts on the environment and on production economics. In Northern Europe, dairy cattle are mainly fed forage-based diets supplemented with protein feeds such as rapeseed meal. This thesis sought to develop and evaluate new methods for forage protein evaluation and to improve the value of locally produced protein feeds. Ruminal metabolism of the grass silage soluble nitrogen (SN) fraction and of 15N-labelled ammonia was modelled based on degradation kinetics determined in vivo. Kinetic models were developed to provide an optimal fit between predicted and observed values of 15N atom excess in different rumen N pools. Microbial N synthesis was around 20% greater with soluble non-ammonia N (SNAN) than with ammonia N, proving that SNAN stimulates microbial growth. The protozoal contribution to direct protein degradation in cows fed at high intake was rather small, with around 95% of protozoal N originating from bacterial N. An estimated 12.5% of SNAN escaped ruminal degradation. The in vitro degradation rates of SN fractions were very similar to those observed in other in vitro studies, but much lower than those measured in vivo. Immediate predicted microbial uptake of SN in grass silage was similar to that observed in vivo (20% and 14%, respectively), but significantly greater for red clover SN fractions (> 50%). Proportionally more grass silage insoluble N was degraded (detected) to ammonia N than of red clover, and of dried forages than of silage. Dried forage had a higher concentration of utilisable crude protein (uCP) than silage. Heat treatment of legume seeds (field bean, lupin and peas) increased uCP concentrations, but high temperatures (over 140°C in oven or 120°C in autoclave for more than 30 min) also significantly increased the indigestible N fraction in the feeds. The in vitro method shows potential for estimating uCP concentrations, but requires further development to estimate degradation of proteins in vivo. Using 15N-labelled forages is a promising method for future protein metabolism studies.
SPATIOTEMPORAL ANALYSIS OF GENE FLOW PATTERNS AMONG WOODLAND SALAMANDER POPULATIONS INHABITATING CONTRASTING LANDSCAPES

Dispersal is a fundamental evolutionary process that serves as a mechanism by which local populations remain connected through space. Habitat loss and fragmentation remain widespread threats to biodiversity globally, and therefore it is imperative to understand how dispersal patterns are affected by anthropogenic modifications of the environment. Using a panel of 10 novel microsatellite loci, I estimated gene flow patterns over historical and contemporary timescales among populations of Eastern Red-backed Salamanders (Plethodon cinereus) in a previously unstudied portion of the species range. Four focal populations reside within a highly fragmented urban center whereas the remaining four focal populations persist in a relatively continuous landscape. Among fragmented populations, I observed weak genetic structuring, primarily driven by a highly divergent population. In contrast, populations in the continuous landscape were genetically homogeneous. Temporal analysis of gene flow patterns within the fragmented landscape revealed little difference between historical and contemporary estimates, as well as gene flow estimates comparable to those observed in continuous habitat. These results suggest that the observed genetic differentiation is not a result of reduced gene flow following fragmentation. In the continuous landscape, temporal changes in gene flow indicate a re-routing in the directionality of the major source of historical migrants, likely corresponding to historical land use practices. In both landscape types, I found the contribution of historical processes to be important in shaping contemporary gene flow patterns, as well as gene flow occurring on a large scale within a fragmented landscape.
Torturing Molecular Motors: Single-Molecule Studies of Viral Packaging and Flagellar Switching

Author(s): Politzer, Adam Terrall | Advisor(s): Liphardt, Jan T | Abstract: Molecular motors play a central role in all known living systems. Cells use them to fight the never ending battle against entropy. Motors allow cells to organize their components in space and time to perform complex functions. In this thesis I focus on two molecular motors: the packaging motor of phi29, and the flagellar motor of Escherichia coli. These are both well-studied motors with decades of research poured into them. By leveraging past knowledge, I was able to undertake subtle studies of their function. I tortured these motors by putting them in sub-optimal operating conditions to test their limits.For the phage motor we were primarily interested in what sort of contacts it uses to engage and exert force on its DNA substrate. We queried the nature of these contacts by making a series of modified DNA substrates, with a focus on methylphosphonate substitutions that maintain the structure of DNA while removing the negative charge. Interestingly, we found that the negative charge of the phosphates was not required for the motor to translocate DNA, but that the charge stabilizes the interaction and makes the motor less likely to slip. We also discovered that the motor interacts more strongly with one of the DNA strands, and we used these modifications to identify a set of periodic contacts.For the flagellar motor I was interested in the role of proton motive force (PMF) in changing the rotational direction of the motor, which is controlled by a complex on its cytoplasmic side called the flagellar switch. The motor is powered by PMF, but does the PMF also affect the switch? We found that in fact the switch is affected by changes in PMF. This has implications for the switching mechanism. The switch is not only affected by the chemical binding signal, but is also affected by its associations with the motor and potentially its proximity to charges on the cell membrane.
Chaparral bird community responses to prescribed fire and shrub removal in three management seasons

1Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, USA; 2School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA; 3Pacific Wildland Fire Sciences Lab, US Forest Service, Seattle, WA, USA; 4Bouverie Preserve, Audubon Canyon Ranch, Glen Ellen, CA, USA; 5Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA and 6University of California Hopland Research & Extension Center, Hopland, CA, USA
Using non - negative matrix factorisation to facilitate 1 efficient bird species richness surveys 2

3 This paper considers the task of learning spectra of bird vocalisations to facilitate determination of unique 4 species from environmental recordings. Although a variety of automated methods have been successfully 5 applied for acoustic recognition of specific bird species, they normally require a well labelled training dataset. 6 However, such methods are less effective in case of non-targeted multi-species inventories. 7 In this study, we propose a non-negative matrix factorisation based clustering method to address this problem. 8 First, the non-negative matrix factorisation is applied to decompose spectrogram matrices into temporal 9 coefficient matrices and spectral profile matrices. By clustering temporal coefficients of a spectrogram matrix, 10 we average the corresponding spectral profiles that fall into the same clusters as distinct bird vocalisations. 11 Under the assumption that no species share similar vocalisations and any species has a low diversity of 12 vocalisations, we utilise the spectral profiles to indicate distinct bird species. A greedy algorithm is then 13 designed to sample audio clips so that each audio clip maximise the number of new spectral profiles. One is 14 enabled to enhance the efficiency of determining the bird species richness from environmental recordings. The 15 efficiency is validated with bird annotations provided by experienced ornithologists. 16
Participation in planning and social networks increase social monitoring in community‐based conservation

Biodiversity conservation is often limited by inadequate investments in monitoring and enforcement. However, monitoring and enforcement problems may be overcome by encouraging resource users to develop, endorse, and subsequently enforce conservation regulations. In this article, we draw upon the literature on common‐pool resources and social networks to assess the impacts of participation and network ties on the decisions of fishers to voluntarily report rule violations in two Jamaican marine reserves. Data was collected using questionnaires administered through personal interviews with fishers (n = 277). The results suggest that local fishers are more likely to report illegal fishing if they had participated in conservation planning and if they are directly linked to community‐based wardens in information sharing networks. This research extends well‐established findings regarding the role and impacts of participation on biodiversity conservation by highlighting the importance of synergies between participation and social networks for voluntary monitoring of conservation regulations.
PHYLOGENETIC RELATIONSHIPS OF INDONESIAN BANANA CULTIVARS INFFERED FROM TRNL-F INTERGENIC SPACER OF CHLOROPLAST DNA

A phylogenetic relationship of Indonesian banana cultivars was conducted using trnL-F intergenic spacer of chloroplast DNA sequences. The ingroup was 39 banana accessions from various genomic groups in Indonesia consisting of 9 AA/AAA; 11 AAA; 2 BB; 13 AAB; and 4 ABB cultivars and 12 sequences of different taxa of Musa downloaded from GenBank consisting of 4 AA wild; 1 AA; 3 AAB; and 4 ABB cultivars. Two accessions from section Rhodoclamys and Australimusa were used as the outgroup. The 39 accessions of the ingroup and the 2 accessions of the outgroup were analyzed using primers of the trnL-F intergenic spacer. The results showed that sequence of the trnL-F region can clearly distinguish 40 banana accessions having the A-type chloroplast (AA wild; AA; AA/AAA; AAA; AAB; and ABB) from those 11 accessions having the B-type chloroplast (BB, AAB, and ABB). The A-type chloroplast accessions are most probably derived from female Musa acuminata, while the B-type chloroplast accessions may be derived from female M. balbisiana. However, the specific M. acuminata ancestor of each cultivar remains unidentified.
Review of Dry Matter Production and Light Interception by Plants for Yield Improvement of Greenhouse Tomatoes in Japan

The fresh fruit yield of tomatoes (Solanum lycopersicum L.) is determined by yield components and related traits. In a lowtruss cultivation in Japan, there was no significant difference in light use efficiency between different planting densities and stages. Accordingly, dry matter production is described by a function of intercepted light: Total dry-matter production = light use efficiency × Intercepted light. Light interception is determined by leaf area index (LAI) and the light extinction coefficient in the plant canopy. The efficiency of dry matter production per unit of intercepted light, i.e., light use efficiency, is determined by not only the leaf photosynthetic rate but also light extinction coefficient. The higher yield of modern tomato cultivars in The Netherlands is due to the increase in total dry matter production of plants, not by an increase in dry matter partitioning to fruits. An increase in the photosynthetic rate and a decrease in the light extinction coefficient may result in an increase in light use effi ciency among Dutch cultivars. The yield of greenhouse tomatoes in Japan has increased little since the 1980s. Recently, Japanese researchers have attempted to improve the yield using current Japanese cultivars. Elevation of CO2 and fogging in a greenhouse improved the fresh fruit yield and total dry matter production in Japanese cultivars. However, the fraction of dry matter distribution to fruit in ‘Momotaro York’ was significantly decreased. The fruit yield was also improved by grafting the Japanese scion ‘Momotaro York’ onto Dutch rootstock ‘Maxifort’ (S. lycopersicum × S. habrochaites). The increases in yield and total dry matter production were mainly determined by the increase in light use efficiency.
VERNALISATION IMPACT ON BIOMETRICAL PARAMETERS OF FESTULOLIUM VARIETIES

Many plants, including Festulolium , grown in temperate climates require vernalization and must experience a period of low winter temperature to initiate or accelerate the flowering process. The aim of research was to investigate impact of vernalisation thermoinduction on growth and development parameters of Festulolium new varieties ’Vėtra’ and ’Punia’. Investigations were carried out in Lithuanian Research Centre for Agriculture and Forestry Institute of Horticulture, Plant Physiology Laboratory of phytotron complex in 2011-2012. The aim of research is to investigate some peculiarities of growth and development of Festulolium . Festulolium varieties ’Vėtra’ and ’Punia’ were investigated. 5 plants were sown in each 5 liter pot in neutral peat substrate (pH 6-6.5). The plants were grown in greenhouse till the tillering phase at the temperature of 20±2°C at daytime and 16±2°C at night. Later plants were moved to low temperature chambers for 90, 110 and 130 days for passing of vernalisation processes, where the 8 and 16 hour photoperiod were maintained at 4°C temperature. After vernalisation periods plants were removed to a greenhouse for additional 20 days. Biometric parameters, namely plant height, shoot number, and dry mass were measured after each period in greenhouse and climatic chambers. The data revealed different response of Festulolium new varieties ’Vėtra’ and ’Punia’to vernalisation conditions.According to our data ’Vėtra’ plant height was 6% higher than the ’Punia’ after 130+20 days of vernalisation. Nonetheless, vernalisation temperature conditions have no significant impact on shoot number. 110 and 130 long-day photoperiod significantly impacted on shoot number of Festulolium ʽVėtraʼ. Otherwise, 90 days vernalisation of both photoperiod induced significantly the highest length of ʽPuniaʼ shoots. ʽVėtraʼ accumulated significantly the maximum dry matter after 110 days vernalisation period, than that after 90 and 130 days. Keywords: Festulolium, vernalisation, photoperiod, morphometry Article DOI: http://doi.org/10.15544/RD.2017. 002
Diversité des relations affiliatives chez les ovins en situation d’élevage : mécanismes comportementaux et neurobiologiques

Les ovins sont bien connus pour développer différentes formes d’attachement social. Le déclenchement de la motivation maternelle et le développement d’un lien mutuel entre la mère et son jeune sont sous l’influence combinée de stimulations hormonales et somato-sensorielles périphériques. Ces stimulations sont fournies par la parturition chez la mère et par les premiers épisodes de tétée chez le nouveau-né. Des changements neurophysiologiques profonds sont observés dans les bulbes olfactifs principaux de la brebis, alors qu’ils sont exposés à des odeurs d’agneau nouveau-né. L’activation de l’hypothalamus consécutive à la mise bas contribue à l’expression de la motivation maternelle et à la mémorisation des odeurs de l’agneau. L’hypothalamus et l’amygdale sont également activés chez le nouveau-né suite à l’ingestion de colostrum. L’ocytocine, un neuropeptide connu pour jouer un rôle clé dans les comportements prosociaux, facilite la construction de la relation mère-jeune. Lorsque des agneaux nouveau-nés sont séparés de leur mère pour être artificiellement nourris, une pratique agricole très commune, ils sont profondément affectés. Les réponses neuroendocrinologiques suggèrent que les agneaux sont dans une situation de détresse. Cependant, si un humain prend soin d’eux, une liaison interspécifique se met en place, facilitée par des contacts sociaux positifs dans lesquels l’allaitement au biberon ou les caresses jouent un rôle clé. De tels contacts activent le système ocytocinergique, comme cela est observé dans la construction du lien mère-jeune. Ainsi, dans des conditions d’élevage artificiel, l’être humain devient une figure d’attachement saillante qui se substitue à la mère et qui peut faciliter la gestion des agneaux.
Looking back to move forward - a personal perspective on pig molecular genetics from RFLPs to nextgen sequencing

My first foray into porcine molecular genetics commenced about 27 years ago with a small Australian Research Council grant to develop and exploit DNA markers in the pig for genetic mapping. At that stage, the standard procedure for detection of DNA polymorphism involved digestion of genomic DNA with one or more restriction enzymes, electrophoresis, transfer to a membrane, hybridisation with a radioactively labelled probe (using dangerous radioactive phosphorous) and autoradiographic detection on an X-ray film. The detection of these restriction fragment length polymorphisms (RFLPs) was slow, insensitive, expensive and hazardous, but was an important starting point and enabled initial molecular studies of porcine stress syndrome and early contributions to the international PiGMaP Consortium established in 1991 to develop a comprehensive linkage map for the pig. The Pig Research and Development Corporation, later to become Australian Pork Limited, soon began to fund research in my laboratory, continuing up until 2005, with continuous funding of a postdoctoral position from 1992, initially for Paul Le Tissier and subsequently for Yizhou Chen. This funding went on to enable a multi-institutional program of co-operative research involving Universities of Sydney, Melbourne and New England as well as the industry partner QAF (Bunge) Meat Industries in search of quantitative trait loci (QTL) for important traits involved in growth and productivity, meat quality and immune function.
Determining the impact of putative loss-of-function variants in protein-coding genes

Variants predicted to result in the loss of function (LoF) of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. Here, we present ALoFT (Annotation of Loss-of-Function Transcripts), a method to annotate and predict the disease-causing potential of LoF variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between LoF variants deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. When applied to de novo pLoF variants in autism-affected families, ALoFT distinguishes between deleterious variants in patients and benign variants in unaffected siblings. Finally, analysis of somatic variants in > 6,500 cancer exomes shows that pLoF variants predicted to be deleterious by ALoFT are enriched in known driver genes.
Characterization of transcription factors in monogenic disorders of speech and language

Mutations affecting the transcription factor FOXP2 cause a rare form of severe speech and language disorder. Although it is clear that sufficient FOXP2 expression is crucial for normal brain development, little is known about how this transcription factor is regulated. To investigate post-translational mechanisms for FOXP2 regulation, we searched for protein interaction partners of FOXP2, and identified members of the PIAS family as novel FOXP2 interactors. PIAS proteins mediate post-translational modification of a range of target proteins with small ubiquitin-like modifiers (SUMOs). We found that FOXP2 can be modified with all three human SUMO proteins and that PIAS1 promotes this process. An aetiological FOXP2 mutation found in a family with speech and language disorder markedly reduced FOXP2 SUMOylation. We demonstrate that FOXP2 is SUMOylated at a single major site, which is conserved in all FOXP2 vertebrate orthologues and in the paralogues FOXP1 and FOXP4. Abolishing this site did not lead to detectable changes in FOXP2 subcellular localization, stability, dimerization or transcriptional repression in cellular assays, but the conservation of this site suggests a potential role for SUMOylation in regulating FOXP2 activity in vivo. 1 This chapter has been published as: Estruch, S.B. , Graham S.A. , Deriziotis P., Fisher S.E. (2016). The language-related transcription factor FOXP2 is post-translationally modified with small ubiquitinlike modifiers. Scientific reports, 6:20911. 10.1038/srep20911.
Reducing chemical fertilizer use mitigates obstacles in intensive monocropping of cucumber: a probable role of Pseudomonads in the process

ABSTRACT A five-year continuous monocropping of cucumber in a greenhouse receiving 50% NPK and 100% NPK was conducted to explore if reducing chemical fertilizer use can mitigate obstacles in intensive monocropping, and the microbial mechanism of the process. Significant decreases in living seedling rates and total yields with time were exhibited in the 100% NPK treatments, showing an obvious obstacles event, which can be mitigated by reducing fertilizer use. It was found that both total yields and living seedling rates were negatively correlated with the proportion of Fusarium oxysporum f. sp. cucumerinum (a known cucumber wilt pathogen) in F. oxysporum, suggesting the two fungal groups out of balance in the rhizosphere, was the key factor for the decline in cucumber growth in the monocropping system. Furthermore, the abundance of pseudomonas group, not hydrogen cyanide- or phenazine-producing pseudomonas, can act as the defender against possible fungal pathogens. The opposite relationships between HCN-producing pseudomonas and two plant indicators (cucumber yield and living seedling rate) suggested that HCN-producing pseudomonas exerted positive effects only when cucumber plants’ density was above a certain threshold. The Redundancy Analysis (RDA) showed that changes in soil microbial population size, especially in pseudomonas groups, contributed to the mitigation process.
Technologies of high-throughput tissue-specific gene expression profiling

Gene expression profiling is an important strategy to study animal development, response to stimuli and diseases. RNAs measured in gene expression profiling experiments are frequently purified from mixture of multiple cell types. The resultant data have low resolution, incapable of distinguishing transcriptome of different cell types and likely biased towards up-regulated genes in dominant tissues. These problems can be solved by obtaining tissue-specific gene expression profile. For dozens of years, there have been several strategies developed to isolate specific tissues or purify RNAs from tissue of interest, and combined with high-throughput RNA assays to generate transcriptome of various specific tissues or cell types. This review will introduce basic principles of these methods and their application in large-scale transcriptome analysis, and discuss on their advantages and limitation.