Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying the best climatic predictors in ecology and evolution

Ecologists and many evolutionary biologists relate the variation in physiological, behavioural, life‐history, demographic, population and community traits to the variation in weather, a key environmental driver. However, identifying which weather variables (e.g. rain, temperature, El Niño index), over which time period (e.g. recent weather, spring or year‐round weather) and in what ways (e.g. mean, threshold of temperature) they affect biological responses is by no means trivial, particularly when traits are expressed at different times among individuals. A literature review shows that a systematic approach for identifying weather signals is lacking and that the majority of studies select weather variables from a small number of competing hypotheses that are founded on unverified a priori assumptions. This is worrying because studies that investigate the nature of weather signals in detail suggest that signals can be complex. Using suboptimal or wrongly identified weather signals may lead to unreliable projections and management decisions. We propose a four‐step approach that allows for more rigorous identification and quantification of weather signals (or any other predictor variable for which data are available at high temporal resolution), easily implementable with our new R package ‘climwin’. We compare our approach with conventional approaches and provide worked examples. Although our more exploratory approach also has some drawbacks, such as the risk of overfitting and bias that our simulations show can occur at low sample and effect sizes, these issues can be addressed with the right knowledge and tools. By developing both the methods to fit critical weather windows to a wide range of biological responses and the tools to validate them and determine sample size requirements, our approach facilitates the exploration and quantification of the biological effects of weather in a rigorous, replicable and comparable way, while also providing a benchmark performance to compare other approaches to.
The complete mitochondrial genome of Calliptamus abbreviatus Ikovnnikov (Orthoptera: acridoidea)

Abstract Calliptamus abbreviatus Ikovnnikov (Orthoptera: Acridoidea) is one of the important pests in the grasslands in northern China. The complete mitochondrial genome of this insect was sequenced. This genome is 16,615 bp long, with an AT content of 73.3%, containing 37 typical animal mitochondrial genes and an AT-rich region. All 13 PCGs share the start codon ATN, and the usual termination codons (TAA) are found from 13 protein-coding genes. All of the 22 typical animal tRNA genes were found in C. abbreviatus mt-genome, and most of the tRNAs could be folded into the classic cloverleaf secondary structure except for tRNA-Ser (AGN), which lacks the dihydrouracil (DHU) stem. The sizes of the large and small ribosomal RNA genes are 1555 and 799 bp long, respectively. The AT content of the AT-rich region is 87.0%. Phylogenetic analysis supports that the coleopteran insects from the same family cluster in the same group.
Distribution of Polyarthra vulgaris Carlin (Rotifera: Monogonota) in a warm monomictic lake of Kashmir India

The paper describes seasonal changes in the abundance of Polyarthra vulgaris Carlin (Rotifera: Monogonota) in a warm monomictic water body of Kashmir — Lake Manasbal. The lake is alkaline, generally with low nutrient content. P. vulgaris is a perennial rotifer in the lake and shows higher population density in the open _water area. It prefers a temperature range of 9-18°C and avoids warmer waters with pH>8.5. Besides the abiotic factors, its population appears to be influenced by the abundance of other zooplankters, especially that of Diaphanasoma brachyuruni Lieven (Cladocera).
Investigating the Structure of FtsZ to Understand its Functional Role in Bacterial Cell Division

Investigating the Structure of FtsZ to Understand its Functional Role in Bacterial Cell Division by Desmond Antoine Moore Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Harold P. Erickson, Supervisor ___________________________ Steve B. Haase ___________________________ Meta J. Kuehn ___________________________ Terrence G. Oas ___________________________ Pei Zhou An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry in the Graduate School of Duke University 2016 Copyright by Desmond Antoine Moore 2016
Distribution ranges and spring phenology explain late frost sensitivity in 170 woody plants from the Northern Hemisphere

AimCold events determine the distributional range limits of woody species. Despite global warming, the magnitude of late frost events in boreal and temperate regions is not expected to change. Hence, the risk for late spring frost damage of woody species may increase with an earlier onset of the growing season. Here, we investigated biogeographical, phenological and phylogenetic effects on late frost sensitivity. LocationEcological-Botanical Gardens Bayreuth, Germany (49 degrees 5545N, 11 degrees 3510E). MethodsWe inspected 170 woody species in the Ecological-Botanical Gardens from across the entire Northern Hemisphere for frost damage after an extreme late frost event in May 2011 (air temperature -4.3 degrees C after leaf unfolding of all species). Distribution range characteristics, climatic parameters of place of origin and phenological strategy were linked to sensitivity to the late frost event. ResultsThe northern distribution limit and the range in continentality across the distributional ranges correlated negatively with a taxon's late frost sensitivity (pseudo-R-2=0.42, pseudo-R-2=0.33, respectively). Sensitivity to the late frost event was well explained by the climatic conditions within species' native ranges (boosted regression trees;receiver operating characteristic 0.737). Average (1950-2000) May minimum temperature in species' native ranges was the main explanatory variable of late frost sensitivity (51.7% of explained variance). Phylogenetic relatedness explained additional variance in sensitivity to the late frost event. Sensitivity to the late frost event further correlates well with species phenological strategy. Frost-tolerant species flushed on average 2 weeks earlier than frost-sensitive species. Main conclusionsRange characteristics and the prevalent climatic parameters across species native ranges are strongly related to their susceptibility to late spring frost damage. Further, more late frost-sensitive species unfolded their leaves later than more tolerant species and late frost tolerance is phylogenetically conserved. Thus, late frost sensitivity may challenge natural and human-assisted migration of woody species under global warming.
COMBINAÇÕES DE CULTIVARES DE COENTRO E RÚCULA EM BICULTIVO CONSORCIADAS COM CULTIVARES DE CENOURA

O objetivo deste trabalho foi avaliar combinacoes de cultivares de coentro e rucula em bicultivo consorciadas com cultivares de cenoura em faixas, nas condicoes de Mossoro - RN. O trabalho foi realizado na Fazenda Experimental Rafael Fernandes de julho a dezembro de 2014. O delineamento experimental foi em blocos completos casualizados, com quatro repeticoes e os tratamentos arranjados em um esquema fatorial com tratamentos adicionais do tipo 2 x 2 x 2 + 2. Os tratamentos consistiram da combinacao de duas cultivares de coentro (Verdao e Portugues) e duas cultivares de rucula (Cultivada e Folha Larga), consorciadas com duas cultivares de cenoura (Brasilia e da Esplanada), mais dois tratamentos adicionais, onde o primeiro sao as cultivares em monocultivo e o segundo os sistemas de cultivo (solteiro e consorciado). Foram avaliadas massa fresca e seca da parte aerea em coentro e rucula e massa fresca e seca da parte aerea, bem como, massa de raizes seca, produtividade de raizes comercial e total e produtividade de raizes classificadas na cenoura. No sistema de consorcio avaliaram-se: indice de uso eficiente da terra, indice de eficiencia produtiva, e escore da variavel canonica, alem dos indicadores de eficiencia economica (renda bruta, renda liquido, taxa de retorno e indice de lucratividade). A maior eficiencia agroeconomica nos sistemas consorciados foi conseguida com a combinacao da cultivar de coentro 'Verdao' e as cultivares de rucula 'Folha Larga' ou 'Cultivada', bem como, as cultivares de cenoura 'Brasilia' ou 'Esplanada'. Independentemente das combinacoes das cultivares testadas, sistemas com coentro e rucula em consorcio com cenoura mostraram maior eficiencia do que os monocultivos.
Host plants mixture and fitness of Kolla paulula: with an evaluation of the application of Weibull function

The xylem‐feeding leafhopper Kolla paulula (Walker), a vector of Pierce's disease, occurs primarily on weeds in and around fruit and ornamental crop orchards in Taiwan. Because our preliminary studies showed that K. paulula performed poorly when reared on pilose beggarticks (Bidens pilosa L. var. radiata) (PB) or trilobate wedelia (Wedelia triloba (L.)) (TW) alone, we collected the life table data of K. paulula reared on a mixture of both host plants to determine the effect at the population level. During their lifespan, 95.6% of feeding time was spent on the major host plant (PB) and only 4.4% on the minor host plant (TW). The intrinsic rate of increase (r), finite rate of increase (λ), net reproduction rate (R0) and mean generation time (T) of K. paulula were 0.0487, 1.0500 day−1, 35.86 offspring and 73.4 days, respectively. Because more than 95% of the insects have been observed feeding on both plants, this would indicate that the minor host plant may play an important role in the fitness of K. paulula regardless of the short feeding time. We calculated the percentage contribution to the population parameters made by females that had fed on both PB and TW and compared these with the values obtained for offspring of females that had fed solely on PB. We also evaluated the usefulness of applying the Weibull distribution in demographic studies. We demonstrated that when there is a higher mortality in specific life stages, the fitted Weibull distribution would be inaccurate in describing the survival curve and that application of the fitted curve to the calculation of life expectancy or other statistics would result in significant discrepancy to the actual curve.
Phenotypic Analysis of Gene Expression in Proposed Populus Root Development and Growth Genes.

WEAR, EMILY ELIZABETH. Phenotypic Analysis of Gene Expression in Proposed Populus Root Development and Growth Genes. (Under the direction of Dr. Barry Goldfarb.) Trees fix carbon through the process of photosynthesis, and then allocate resources to their roots and shoots. For carbon sequestration purposes, it can be useful to select genotypes that divert more carbon to the root system where it is less susceptible to degradation, and also to select genotypes tailored to specific site conditions. Using genetic transformation in Populus tremula × P. alba hybrid aspen clones, I studied the effect on root growth and development and lateral root initiation of several putative homologous genes from Arabidopsis thaliana. The three genes studied, PLETHORA1 (PLT1), SHORT-ROOT (SHR), and NAC1 were regulated either by over-expression or RNA interference (RNAi) mediated suppression. Putative transformants of PtPLT1, PtSHR, and PtNAC1 RNAi constructs and a PtSHR over-expression construct were screened for phenotypic alterations to the roots and shoots in a tissue culture experiment. Then, a sub-set of lines from each construct was more thoroughly characterized for growth and physiology traits in a growth chamber experiment with water and nutrient limitation treatments. Finally, the relative gene expression levels compared to the wild type (WT) were analyzed for lines in each construct by real-time quantitative reverse-transcription PCR. I found that lines from the RNAi-mediated suppression constructs of PtPLT1, PtSHR, and PtNAC1 showed very limited phenotypic alterations when screened in tissue culture and no phenotype alterations in a growth chamber experiment. Also, none of the lines in the PtPLT1, PtSHR, and PtNAC1 RNAi constructs actually had suppressed gene expression in comparison to the WT. Lines from the PtSHR over-expression construct had reduced growth and biomass in roots and shoots, and reduced photosynthesis and stomatal conductance rates, but increased chlorophyll content in the leaves. I found there was a strong negative relationship between the increased relative gene expression of the PtSHR over-expression construct lines and the severity of their reduced growth. Overall, there was relatively good correlation between the growth traits measured both in tissue culture and growth chambers, except for a few lines that behaved differently under the two environments or were influenced by positional effects. Additionally, the relative gene expression was slightly more correlated with the growth traits measured in tissue culture than with those measured in growth chambers. Phenotypic Analysis of Gene Expression in Proposed Populus Root Development and Growth Genes by Emily Elizabeth Wear A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Master of Science
Sanitary importance of arcobacter

The genus Arcobacter, belongs to the family Campylobacteraceae, along with. Some species, are considered emerging pathogens and have been associated with gastrointestinal diseases and bacteraemia in humans and with diarrhoea, mastitis and abortions in animals. Diarrhoea, is the most common clinical presentation in humans. However, still are not fully defined the routes of transmission, the virulence factors present in pathogenic strains have not been determined and the isolation and identification methods are still deficient. All of these factors contribute to a possible underestimation of the sanitary importance of this genus. In this thesis it has been demonstrated the existence of five new species of this genus. In their differentiation, new tools have been used, such as the Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI TOF) Multilocus Phylogenetic Analysis (MLPA) with concatenated 5 genes (rpoB, gyrB, hsp60, gyrA and atpA). Furthermore, the performance of 5 molecular identification methods was compared and none of them was useful for all the strains studied. In this regard, the updating of 16S rRNARFLP method for the identification of all species proved very useful. Moreover, in this thesis was a great diversity of species of this genus in samples of shellfish and sewage. Both matrices have epidemiological importance; however, they have been poorly studied. It was also demonstrated that the use in parallel of direct culturing and post enrichment, as well as the incubation under aerobic and microaerophilic, enhances the recovery and diversity of arcobacters. Regarding the virulence of Arcobacter spp. , most of them proved to be potential enteropathogens for man, as they showed the presence of virulence factors and were able to adhere and invade human intestinal cells (Caco-2). Finally, it was demonstrated that Arcobacter may be confused with Campylobacter sp. , generating an underestimation of their sanitary importance.
Local Bacteriophage Delivery for Treatment and Prevention of Bacterial Infections

As viruses with high specificity for their bacterial hosts, bacteriophages (phages) are an attractive means to eradicate bacteria, and their potential has been recognized by a broad range of industries. Against a background of increasing rates of antibiotic resistance in pathogenic bacteria, bacteriophages have received much attention as a possible “last-resort” strategy to treat infections. The use of bacteriophages in human patients is limited by their sensitivity to acidic pH, enzymatic attack and short serum half-life. Loading phage within a biomaterial can shield the incorporated phage against many of these harmful environmental factors, and in addition, provide controlled release for prolonged therapeutic activity. In this review, we assess the different classes of biomaterials (i.e., biopolymers, synthetic polymers, and ceramics) that have been used for phage delivery and describe the processing methodologies that are compatible with phage embedding or encapsulation. We also elaborate on the clinical or pre-clinical data generated using these materials. While a primary focus is placed on the application of phage-loaded materials for treatment of infection, we also include studies from other translatable fields such as food preservation and animal husbandry. Finally, we summarize trends in the literature and identify current barriers that currently prevent clinical application of phage-loaded biomaterials. Graphical Abstract
Genetic Diversity of Mitochondrial DNA D-Loop Sequence of Siberian Roe Deer (Capreolus Pygargus) Inhabiting Mongolia

Roe deer, the only species among the twelve wild artiodactyls in Mongolia that is considered to have large population density and vast area of habitat, live in a herd throughout the year. Roe deer play important role for forest biodiversity. Balanced population density of roe deer affects sufficient regeneration and diversity of flora and fauna in forest. Living area of roe deer is getting disrupted by uncontrolled mining and overgrazing. In this case some small population of roe deer might be endangered. Therefore, if phylogenetic analysis among roe deer populations inhabiting Mongolia is carried out, propagation of the small and endangered roe deer population can be promoted. We have amplified and sequenced 1220 nucleotides of the mitochondrial DNA D-loop region in 12 Siberian (Capreolus pygargus) roe deer from 5 localities in Mongolia. The sequences were aligned with 51 published sequences of roe deer mtDNA D-loop region from GenBank by using the CLUSTAL W version 2.1. software. Phylogenetic reconstructions were performed by Maximum likelihood. Calculations and Maximum likelihood and Neighbor-Joining trees construction were conducted using the MEGA 5.1 software based on Kimura â€“ 2 â€“ parameter model considering transitions, transversions, and irrespective of the nucleotide position. Stability of the clustering order was assessed using bootstrap (100 permutations). The alignment showed 20 polymorphic sites including 13 transitions and 7 transversions, defined 12 haplotypes within our samples. The mean nucleotide divergence of roe deer haplogroups was 2.8% between Mongolian and Russian, 3.5% between Mongolian and Korean, 3.5% between Mongolian and Kyrgystani and 2.4% between Mongolian and Chinese roe deer. Phylogenetic tree showed every cluster has haplotypes representing roe deer in Mongolia, which could mean that Mongolia might be the center of migration for Siberian roe deer.
Structural stability of CD1 domain of human mitotic checkpoint serine/threonine-protein kinase, Bub1

Bub1 is one of the spindle checkpoint proteins and plays a role in recruitment of the related proteins to kinetochore. Here, we studied the structural characteristic of the evolutionarily conserved 160 amino acid region in the N-terminus (hBub1 CD1), using Circular Dichroism (CD) and NMR. Our CD results showed that hBub1 CD1 is a highly helical protein and its structure was affected by pH: as pH was elevated to basic pH, the helical propensity increased. This could be related to the surface charge of the hBub1 CD1. However, the structural change did not largely depend on the salt concentration, though the thermal stability a little increased. The previous NMR analysis revealed that the hBub1 CD1 adopts eight helices, which is consistent with the CD result. Our result would be helpful for evaluating the molecular mechanism of the hBub1 CD1 and protein-protein interactions.
Chemiluminescence of blood plasma in the presence of hydrogen peroxide

: Chemoluminescence arised after incubation of diluted blood plasma with hydrogen peroxide. A typical pattern of the luminescence development, similar to that obtained on addition of H2O2 to other biological objects, was observed: quick increase and gradual decrease to a steady-state chemoluminescence level. The increase in chemoluminescence, which was noted in some experiments, might be due to elevation in content of both initiators of peroxidation and activators of the chemoluminescence in blood plasma. Kinetics of the chemoluminescence did not correlate with concentration of oxygen in media.
Captive Breeding of the Shark Bay Mouse Pseudomys fieldi to Facilitate Species Recovery in the Wild

Shark Bay Mice ( P. fieldi ) were bred at Perth Zoo to provide animals for release to the wild as part of recovery actions for the species. Three-hundred and thirty-five young were produced from 93 litters, with an average litter size of 3.6 (range 1 – 6). Sexual maturity for both sexes was reached at 65 days of age, and breeding was observed all year round. The oldest female to give birth was 625 days of age and the oldest male to sire young was 531 days of age. Following a planned interruption to the program and the separation of breeding pairs, there was some difficulty in later re-establishing reproduction. A strategy to stimulate a return to breeding, along with detailed husbandry methods, is described.
Cassava HapMap: Masking deleterious mutations in a clonal crop species

Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America, however, ubiquitous deleterious mutations may severely reduce its fitness. To evaluate these deleterious mutations in the cassava genome, we constructed a cassava haplotype map using deep sequencing from 241 diverse accessions and identified over 28 million segregating variants. We found that, 1) while domestication modified starch and ketone metabolism pathways for human consumption, the concomitant bottleneck and clonal propagation resulted in a large proportion of fixed deleterious amino acid changes, raised the number of deleterious mutations by 26%, and shifted the mutational burden towards common variants; 2) deleterious mutations are ineffectively purged due to limited recombination in cassava genome; 3) recent breeding efforts maintained the yield by masking the most damaging recessive mutations in the heterozygous state, but unable to purge the mutation burden, which should be a key target for future cassava breeding.