Miracle-dz/UniFAR-FTUs huggingface dataset:
Predation risk drives the expression of mobbing across bird species

: Many species approach predators to harass and drive them away, even though mobbing a predator can be deadly. However, not all species display this behavior, and those that do can exhibit different behaviors while mobbing different predators. Here we experimentally assessed the role of social and ecological traits on the expression of mobbing behavior in a bird community in SE Brazil (n = 157 species). We exposed birds to models of two morphologically similar diurnal owls that pose different risks, and assessed which species engaged in mobbing. Among those that mobbed, we evaluated how they adjusted their mobbing behavior depending on the predator type. We tested the hypothesis that only species that are at risk and can afford to mob engage in this antipredator behavior. We found that species that engaged in mobbing are in the body mass range of potential prey, forage in the understory or in the canopy, and form flocks. A species’ social system did not influence its mobbing behavior. Furthermore, species that engaged in mobbing formed larger mobbing assemblages when facing a high-risk predator, but mobbed more intensely when facing a low-risk predator. Our findings support our predictions, namely that the expression of mobbing is limited by its costs. Abstract Many species approach predators to harass and drive them away, even though 43 mobbing a predator can be deadly. However, not all species display this 44 behavior, and those that do can exhibit different behaviors while mobbing 45 different predators. Here we experimentally assessed the role of social and 46 ecological traits on the expression of mobbing behavior in a bird community in 47 SE Brazil (n=157 species). We exposed birds to models of two morphologically 48 similar diurnal owls that pose different risks, and assessed which species 49 engaged in mobbing. Among those that mobbed, we evaluated how they 50 adjusted their mobbing behavior depending on the predator type. We tested the 51 hypothesis that only species that are at risk and can afford to mob engage in 52 this anti-predator behavior. We found that species that engaged in mobbing are 53 in the body mass range of potential prey, forage in the understory or in the 54 canopy, and form flocks. A species’ social system did not influence its mobbing 55 behavior. Furthermore, species that engaged in mobbing formed larger 56 mobbing assemblages when facing a high-risk predator, but mobbed more 57 intensely when facing a low-risk predator. Our findings support our predictions, 58 namely that the expression of mobbing is limited by its costs.
Karyotypes of Five Hylid Frogs from Papua New Guinea, with a Discussion on Their Systematic Implications

The karyotypes of three species of the genus Litoria and two of the genus Nyctimystes (Hylidae: Pelodryadinae) from Papua New Guinea are reported. They have 2n=26 chromosomes which can not be divided into distinct size groups. In Litoria species, five or six pairs among pair Nos. 2-8 are submetacentric or subtelocentric and the others metacentric. The karyotype of Nyctimystes differs from that of Litoria in having a longer No. 1 and metacentric No. 2. Karyological comparisons with related taxa suggest that the Pelodryadinae is most closely related to the Phyllomedusinae, and that the primitive leptodactylids, rather than the Australian myobatrachids, are likely to be the ancestral stock of the Pelodryadinae. Nyctimystes seems to have been derived from a group of Litoria.
Identificação molecular de linhagens de fungos pertencentes aos gêneros Aspergillus, Penicillium e Fusarium utilizando marcadores RAPD.

Microorganisms’ cultures collections present important contribution for the preservation, maintenance and supply of authentic cultures to the researchers. As well, assures a strict control for the acquisition and deposit in the banks of microorganisms and supply subsidies for the researches carried out in a scientific institution. Among the interest of fungi lineages in the industrial and pharmaceutical area and also food stuffs, they are the fungi belonging to the genus Aspergillus, Penicillium and Fusarium. The identification and microbiological characterization and the use of molecular techniques can contributed with the classification and definition of new táxons. The molecular marker RAPD, despite of some limitations, have shown helpful in the studies of microorganisms where does not have a lot genetic information. That work had as main objective, determine the molecular profile and identify RAPD specific markers for lineages of fungi belonging to the genus Aspergillus, Penicillium and Fusarium, in order to contribute to the philogenetic studies, used to determine the common origin among the species.
Construction and Optimization of Tetracycline-Responsive Gene Expression Systems

Conditional gene expression systems that enable inducible and reversible transcriptional control are essential research tools and have broad applications in biomedicine and biotechnology. The reverse tetracycline transcriptional activator is a canonical system for engineered gene expression control that enables graded and gratuitous modulation of target gene transcription in eukaryotes from yeast to human cell lines and transgenic animals. However, the system has a tendency to activate transcription even in the absence of tetracycline and this leaky target gene expression impedes its use. Here, we identify single amino-acid substitutions that greatly enhance the dynamic range of the system by reducing leaky transcription to undetectable levels while retaining high expression capacity in the presence of inducer. Furthermore, we show that these improved DNA binding domains can be fused to repression domains to create synthetic transcriptional repressors. The function of these transcriptional repressors is dependent on the location of their recruitment and their mechanisms of action.
Genetic structure of Culcita sp. pincushion seastar in the Coral Triangle

From the Coral Triangle, which is the global centre of marine biodiversity, species richness tends to decrease eastward across the Pacific Ocean and westward across the Indian Ocean. However, this region is severely threatened by both human and natural disturbances, calling for urgent conservation efforts. Conservation and management decisions inevitably require definition of the limits of population structure of each species as well as mechanisms that produce high biodiversity in the Coral Triangle. In this study we sequenced the mitochondrial COI region of the pincushion seastar, Culcita sp. , a common coral reef seastar whose life history resembles other well-studied coral reef seastars. We found a large genetic difference between Indian (Culcita schmideliana) and Pacific Ocean (Culcita novaeguineae) lineages. All the populations (except from Thailand) had Pacific mtDNA haplotypes, while central and western Indonesian populations had both Indian and Pacific haplotypes, showing a sign of sympatric distribution of these two genetic lineages around these areas. Overall gene flow of Culcita sp. in the Coral Triangle was strong and resembled that of Acanthaster planci with similar life history traits. Further analysis using nuclear marker might reveal possible hybridization between the distinct genetic lineages of the species in this region.
Characterising the role of TLE1 in Crohn’s disease

ix Chapter 1: Introduction . 1 1.1 Inflammatory Bowel Disease . 2 1.2 Structure of the gastrointestinal (GI) tract . 2 1.2.1 Incidence of IBD . 4 1.2.2 Pathogenesis . 4 1.3 Environmental risk factors for IBD . 5 1.4 Genetics of IBD . 5 1.4. 1 Heritability . 5 1.4. 2 Approaches . 6 1.4. 3 The differentiation of Th17 lymphocytes in IBD pathogenesis . 8 1.4. 4 The Unfolded protein response in IBD pathogenesis . 9 1.4. 5 IBD and Autophagy . 10 1.4. 6 NOD2 (Nucleotide Oligomerisation Domain 2) . 11 1.4. 7 Yeast 2 Hybrid Assays . 21 1.5 TLE1 (Transducinlike enhancer of Split) . 23 1.5. 1 TLE1 in Crohn’s Disease . 23 1.5. 2 Discovery and structure of TLE1 . 23 1.5. 3 Expression patterns in different tissues . 25 1.5. 4 TLE1 transcripts . 26 1.5. 5 TLE1 function . 27 1.5. 6 TLE1 in different signaling pathways . 28 1.6 Dysregulation in cancer . 34 1.6. 1 TLE1 deletion in model organisms . 35 1.7 Aims . 36 2 Materials and Methods . 37 2.1 Buffers and solutions . 38 2.1.1 Bacterial culture . 38 2.1.2 Cell culture . 38 2.1.3 Chromatin Immunoprecipitation . 39 2.1.4 Antibodies . 40 2.1.5 Expression vectors . 41 2.2 Bacterial Culture . 41 2.3 Cell culture . 42 2.3. 1 Maintenance of cell lines . 42 2.3. 2 Cell counting . 42 2.3. 3 Long term storage of cells . 43 2.3. 4 Transient transfection . 43 2.3. 5 MDP stimulation . 44 2.4 Protein analysis . 44 2.4. 1 Sample preparation. 44 2.4. 2 Western Blotting . 44 2.5 RNA analysis . 46 2.5. 1 RNA extraction and cDNA conversion. 46 2.5. 2 Real-time Quantitative PCR (RT qPCR) . 46 2.6 DNA Analysis . 48 2.6. 1 DNA Extraction . 48 2.6. 2 Polymerase Chain Reaction (PCR) . 48 2.6. 3 Sanger sequencing . 49 2.7 Statistical Analysis . 49 3 Analysing the effect of knocking down TLE1 and stimulating NOD2 on genome wide expression . 50 3.
Imprinted loci may be more widespread in humans than previously appreciated and enable limited assignment of parental allelic transmissions in unrelated individuals

Genomic imprinting is an epigenetic mechanism leading to parent-of-origin dependent gene expression. So far, the precise number of imprinted genes in humans is uncertain. In this study, we leveraged genome-wide DNA methylation in whole blood measured longitudinally at 3 time points (birth, childhood and adolescence) and GWAS data in 740 Mother-Child duos from the Avon Longitudinal Study of Parents and Children (ALSPAC) to systematically identify imprinted loci. We reasoned that cis-meQTLs at genomic regions that were imprinted would show strong evidence of parent-of-origin associations with DNA methylation, enabling the detection of imprinted regions. Using this approach, we identified genome-wide significant cis-meQTLs that exhibited parent-of-origin effects (POEs) at 35 novel and 50 known imprinted regions (10−10< P <10−300). Among the novel loci, we observed signals near genes implicated in cardiovascular disease (PCSK9), and Alzheimer’s disease (CR1), amongst others. Most of the significant regions exhibited imprinting patterns consistent with uniparental expression, with the exception of twelve loci (including the IGF2, IGF1R, and IGF2R genes), where we observed a bipolar-dominance pattern. POEs were remarkably consistent across time points and were so strong at some loci that methylation levels enabled good discrimination of parental transmissions at these and surrounding genomic regions. The implication is that parental allelic transmissions could be modelled at many imprinted (and linked) loci and hence POEs detected in GWAS of unrelated individuals given a combination of genetic and methylation data. Our results indicate that modelling POEs on DNA methylation is effective to identify loci that may be affected by imprinting.
Toads, tall mountains and taxonomy: the Rhinella granulosa group (Amphibia: Anura: Bufonidae) on both sides of the Andes

A toad in the Rhinella granulosa group has been recognized as present on Trinidad since 1933. In 1965, the Trinidadian population was described as a subspecies of Bufo granulosus, B. g. beebei. It has its type locality on the island and was eventually raised to species status as B. beebei (Beebe’s toad). Recently Beebe’s toad was synonymized with Rhinella humboldti, a species with a type locality in the Magdalena Valley of western Colombia. The Magdalena Valley is separated from the Orinoco Basin by the Eastern and Merida Cordilleras. These ranges have peaks that exceed 5,000 m and an almost continuous altitude at about 3,000 m. Here we examine the morphology, advertisement calls, and mtDNA from several populations of these lowland toads to test whether the western Colombian R. humboldti and the Orinoco-Trinidad R. beebei are conspecific and form a single taxon that occurs on both sides of the Andes. The morphological, molecular, and advertisement call analyses suggest that R. humboldti and R. beebei are distinct taxa composed of independent evolving lineages. Rhinella beebei is therefore resurrected from the synonymy of R. humboldti for the Trinidad and some of the adjacent mainland Orinoco populations in both Venezuela and Colombia. This increases the number of described species in the clade to fourteen. Rhinella humboldti and its sister R. centralis (Panama) are the only members of the R. granulosa group to occur west of the Andes, and our molecular results suggest the TMRCA for R. beebei and R. humboldti at about 9 Mya, a time when the Eastern Cordillera was much lower in altitude than it is today and the Merida Cordillera was in its early stages of formation.
Bottom-up and top-down control of dispersal across major organismal groups: a coordinated distributed experiment

Organisms rarely experience a homogeneous environment. Rather, ecological and evolutionary dynamics unfold in spatially structured and fragmented landscapes, with dispersal as the central process linking these dynamics across spatial scales. Because dispersal is a multi-causal and highly plastic life-history trait, finding general drivers that are of importance across species is challenging but highly relevant for ecological forecasting. We here tested whether two fundamental ecological forces and main determinants of local population dynamics, top-down and bottom-up control, generally explain dispersal in spatially structured communities. In a coordinated distributed experiment spanning a wide range of actively dispersing organisms, from protozoa to vertebrates, we show that bottom-up control, that is resource limitation, consistently increased dispersal. While top-down control, that is predation risk, was an equally important dispersal driver as bottom-up control, its effect depended on prey and predator space use and whether dispersal occurred on land, in water or in the air: species that routinely use more space than their predators showed increased dispersal in response to predation, specifically in aquatic environments. After establishing these general causes of dispersal, we used a metacommunity model to show that bottom-up and top-down control of dispersal has important consequences for local population fluctuations as well as cascading effects on regional metacommunity dynamics. Context-dependent dispersal reduced local population fluctuations and desynchronized dynamics between communities, two effects that increase population and community stability. Our study provides unprecedented insights into the generality of the positive resource dependency of dispersal as well as a robust experimental test of current theory predicting that predator-induced dispersal is modulated by prey and predator space use. Our experimental and theoretical work highlights the critical importance of the multi-causal nature of dispersal as well as its cascading effects on regional community dynamics, which are specifically relevant to ecological forecasting.
Diversidad florística del bosque mesófilo en el norte de Chiapas y su relación con México y Centroamérica

The distribution of woody genera in the montane cloud forest in the northern highlands of Chiapas was registered and compared with other 23 localities in Mexico and Central America. A total of 312 genera in 99 families were recorded. The most diverse families were Rubiaceae (19), Leguminosae (16), Ericaceae ( 15) and Compositae ( 14). Quercus, Clelhra, Cornus, Oreopanax, and Ceslrum were present in more than 95% of the si tes, while 32 genera ( 10%) alone were registe red once. Non-metric multidimentional scaling analysis showed the presence of six groups of localities according to their diversity values and geographical position. Sierra de Manantlan, El Triunfo, Cordillera of Talamanca, and Northern highlands of Chiapas were the most diverse localities. The greater proportion of the genera (41 %) have a meridional distribution (except pantropical), 15% holarctic, 4% american-african, 9% malayan-american, 3% austral-antarctic, 14% pantropical, 5% widely distribution and 9% of the genera are considered exclusive of Mexico and/or Central America.
Role of PTPRT in obesity and its substrate paxillin tyrosine-88 in colorectal cancer

15 Chapter 1: Background and Significance 17 Colorectal Cancer 18 Etiology, staging, and therapy 18 Molecular basis of colorectal cancer 20 Genomics of colorectal cancer 21 PTPRT: Structure and Function 24 PTPRT’s Domain Structure 25 PTPRT’s role in neurological development 26 PTPRT as a tumor suppressor 26 Other Type IIB RPTPs as tumor suppressors 28
Nutrition research agenda in the context of nutrition problems in Tanzania - a critical review

Historically, preventing undernutrition (stunting, wasting and underweight) has proven to be very difficult. Broad, food-based counsel is generally too superficial, and multiple nutrient deficiencies often occur even when food recommendations are followed. Advances in dietary assessment and planning over the past 10 years have enabled more precise estimates of nutrient intake and nutrient need. The recommended nutrient intake (RNI) in areas with high rates of stunting and underweight are now available. However, bioavailability is a major constraint for some nutrients, particularly in plant-based diets when food fortification or the use of nutrient supplements does not occur. Inadequate control of infectious diseases is a major factor limiting nutrient utilization and causing poor development of the immune system in young children. The role of mycotoxins in poor immune system development and poor growth is becoming increasingly apparent, but additional research is needed in this area. A number of key research agendas have been identified, which include the need to identify what nutrients are necessary, other than vitamin A, iodine and iron, which are being consumed in inadequate quantities in Tanzania; to establish a country-specific food composition database; to develop appropriate technologies, which can be easily adopted, for preserving and processing foods; to investigate the effects of exposure to mycotoxins on nutritional status and growth; to identify appropriate complementary foods for Tanzanian children; and to investigate the economics of improving nutritional status by promoting animal-based food products in Tanzania. Others research areas include an investigation into the unique cultural dimensions of dietary intake in Tanzanian society; the nutrient requirements for people who have various common illnesses, such as malaria; and the effects on the nutrient content of foods grown under climate change stresses, e.g., moisture and temperature. Keywords: Nutrition research gap; innovative nutrition research agenda; nutrient bioavailability; Nutrient deficiencies
Gamma irradiation mutagenesis in Monstera deliciosa

Cut foliage of Monstera deliciosa is widely used in flower arrangement due to its long vase life and striking foliage pattern. Variegated Monstera of commercial importance is scarce. Therefore, we examined the potential of mutagenesis in obtaining variegated mutants by gamma ray irradiating the seeds. The germination rate was reduced by increasing the irradiation dosage. The LD50 dosage was between 10 to 25 Gy. We further compared the survival rate of seeds from different source at 0, 7.5, 10, and 12.5 Gy. Dosage higher than 12.5 Gy was required to achieve LD50 germination rate. Next, seeds pre-soaked for 5 days were compared to dry seeds for their sensitivity to gamma irradiation at various dosages (10, 12.5, 15, 17.5, 20, and 22.5 Gy). The highest germination rate was obtained by 10 Gy of dry seeds and 12.5 Gy of soaked seeds. The lowest germination rate was observed by 22.5 Gy for both dry and soaked seeds. The soaked seeds apparently were more tolerant to the damage caused by higher dosage of irradiation. Different pattern of leaf variegation was obtained after gamma ray irradiation, including light green to yellow green sectors.
Spatio-Temporal Variations in Pathogenic Bacteria in the Surface Sediments of the Zuari Estuary, Goa, India

Estuaries are hotspots of anthropogenic activities. The deposition of pathogenic bacteria in the sediment and their re-suspension into the water column are influenced by riverine discharge and tides. The abundance of Escherichia coli O157:H7, Shigella spp. , Salmonella spp. , total coliforms (TC) and Vibrio spp. ( Vibrio cholerae (VC), Vibrio parahaemolyticus (VP), Vibrio alginolyticus (VA)) was assessed along with the total bacterial count (TBC) and total viable count (TVC) in surface sediments along the banks of the Zuari estuary, Goa, India. The study was carried out fortnightly for a period of 17 months covering three seasons, i.e. pre-monsoon (PreM), monsoon (MON) and postmonsoon (POM). The spatial and temporal changes in the quality of organic matter were also assessed. The organic matter content was high and rich in carbohydrates and proteins towards upstream sites. The quality of organic matter was influenced by the seasons. E. coli O157:H7 was detected only during MON towards the upstream stations. A negative correlation between TC and TBC with salinity was evident indicating the influence of land run-off. The Shigella spp. and VA were high towards the mouth of the estuary during PreM. However, during POM, the TVC, TC and VP were abundant towards the upstream and VC were abundant at the mouth of the estuary. Among the Vibrios, VP and VA were the most frequently occurring bacteria whereas TC and Shigella spp. were dominant among allochthonous pathogens in the sediments irrespective of space and time. In addition to influence of seasons, the sampling time influenced by tidal condition also played an important role in the population dynamics of pathogenic bacteria in the sediments. Future studies should address the interaction of pathogenic bacteria with suspended particles, their transport and survival in the sediments.