Miracle-dz/UniFAR-FTUs huggingface dataset:
The Causes and Consequences of Community Disassembly in Human Modified Tropical Forest: Scarabaeine Dung Beetles as a Model System

Biodiversity loss can precipitate extinction cascades and impair ecological processes. These ‘downstream’ effects will be exacerbated if functionally important taxa are tightly linked with species threatened by extinction or population decline. We review the current evidence that such a scenario is currently playing out in the linked declines of persistently hunted mammal populations and the dung beetles communities (Coleoptera: Scarabaeidae: Scarabaeinae) that depend on them for adult and larval food resources. Through a close evolutionary association, mammal assemblages have played a fundamental role in structuring extant dung beetle communities. Today many game mammal species’ populations are severely depleted by subsistence or commercial hunting, especially in tropical forest systems. Multiple lines of evidence from temperate and tropical systems indicate that the regional-scale decline or extirpation of medium and large bodied mammal faunas can severely disrupt the diversity and abundance of dung beetle communities through alterations in the composition and availability of dung resources. These observed community disassemblies have significant shortand long-term implications for the maintenance of key ecosystem processes including nutrient recycling and secondary seed dispersal. Identifying the speciesand community-level traits that buffer or exacerbate these species and functional responses is essential if we are to develop a better understanding of the cascading ecological consequences of hunting in tropical forests.
Structural Bioinformatics: Transforming protein structures into biological insights

Structural bioinformatics is an area that has emerged to comprehend and interpret large amounts of structural data, and promises to provide a high resolution understanding of biology. Protein structures can be compared, analyzed and mined in various ways, which allows us to understand the functions of these molecules and reason precisely how and why such capabilities have emerged in them. The main advantages these methods have over simpler sequence based methods are that besides helping in associating a molecule with a function, they also provide ultimate insights into the mechanisms by which various biological events take place. This report provides an overview of structural bioinformatics, various advances in the recent years and the range and scope of data driven protein structural analysis. In particular, current trends in structure prediction, structure alignments, deriving sub-structures and structural motifs, understanding features critical for molecular recognition as well as using these for understanding function of protein molecules are presented. Application of structural knowledge in drug discovery for lead identification as well as novel ways of understanding drug adverse effects and drug resistance are also discussed. Finally prospects for structure based vaccine design are also outlined. The various aspects of structural bioinformatics discussed here, show how biological insights can be obtained from protein structures.
Variability in enzyme activities of Trichoderma spp.

The effect of different substrates as carbon sources on enzyme activities of Trichoderma spp.in minimum synthetic medium (MSM) was studied. There was marked improvement in the chitinase activities of Trichoderma spp. when the medium was supplemented with either chitin or mycelial powder of M. phaseolina or S. rolfsii,  -1, 3 glucanase,  -1, 4 glucanase, and cellulase activities of Trichoderma spp were also significantly enhanced with addition of glucan, CMC (Carboxymethyl cellulose) and mycelial powder of Pythium aphanidermatum in the basal medium, respectively. The isolate TvAN-3 was most efficient with highest chitinase activity when this isolate was grown in medium supplemented with colloidal chitin (26.5 and 37.0 Pkat/ ml), mycelial powder of M. phaseolina (19.0 and 29.5 Pkat/ml) and S. rolfsii (19.0 and 28.8 Pkat/ml), followed by TvAN-5, ThrAN- 5, ThrAN-7, ThrWB-1 and the isolate ThmAN-10 and ThrWB-2 were the lowest chitinase producers under similar conditions. Highest  -1, 3 and  -1, 4 glucanase activities were expressed with ThrAN-5 (13.6 and 14.9 nkat/ml) and ThrWB-2 being the lowest enzyme activity of only 6.4 and 7.5 nkat/ml. ThmAN-4 was most efficient in secreting cellulase in the culture medium irrespective of other carbon sources. The other best isolates of Trichoderma were ThrAN-5, TvAN-3, TvAN-5, ThmAN-10, ThrAN- 7, ThrWB-1; and TvAN-8 being the least effective isolate in view of their cellulase activities.
Kinetics of batch microbial degradation of phenols by indigenous binary mixed culture of Pseudomonas aeruginosa and Pseudomonas fluorescence

The potential of various organisms to metabolize organic compounds has been observed to be a potentially effective means in disposing of hazardous and toxic wastes. Phenolic compounds have long been recognized as one of the most recalcitrant and persistent organic chemicals in the environment. The bioremediation potential of an indigenous binary mixed culture of Pseudomonas aeruginosa and Pseudomonas fluorescence was studied in batch culture using synthetic phenol in water in the concentration range of 100 –500 mg/L as a model limiting substrate. The effect of initial phenol concentration on the degradation process was investigated. Phenol was completely degraded at different cultivation times for the different initial phenol concentrations. Increasing the initial phenol concentration from 100 to 500 mg/L increased the lag phase from 0 to 18 h and correspondingly prolonged the degradation process from 24 to 96 h. There was decrease in biodegradation rate as initial phenol concentration increased. Fitting data into three different kinetic models (Monod, Haldane, and Yano and Koga) showed that the difference in fit between the models was very small and thus statistically insignificant. Thus, the Yano and Koga model has been used to interpret the free cell data on phenol biodegradation. The kinetic parameters have been estimated up to initial phenol concentration of 500 mg/L. The rsmax decreased, while Ks and Ki increased with higher concentration of phenol. The r smax has been found to be a strong function of initial phenol concentration.
Pollination Biology of Hydnora africana Thunb. (Hydnoraceae) in Namibia: Brood‐Site Mimicry with Insect Imprisonment

Hydnora africana is a root holoparasite of southern Africa that emerges only to flower. The trimerous flowers of H. africana have androecial and gynoecial chambers and attract floral visitors with putrid odors emitted from prominent osmophores. We observed floral phenology and insect visitation for H. africana at two sites in southern Namibia and evaluated the insect imprisonment mechanism with beetle addition and pollen viability assays. Flowers are putatively protogynous for 3 d. We observed 18 floral visitors, including 10 coleopteran species imprisoned by the smooth inner surface of the androecial chamber. The hide beetle Dermestes maculatus (Tenebrionidae) accounted for 76.9% of the imprisoned insects, with a density of \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$2.2\pm 0.6$$ \end{document} per flower. The D. maculatus addition experiment ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$n=9$$ \end{document} ) clearly demonstrated imprisonment during the carpellate stage. Changes in the inner surfaces of the androecial chamber, stippling, and texturing allowed D. maculatus to escape after pollen release. More than 55.5% of the beetles escaped, dusted with pollen, within 3 d after pollen release. Pollen was still viable 3 d after pollen release. The beetle addition and pollen assays demonstrate the efficiency of the H. africana imprisonment mechanism.
Critical period of sensitivity to petroleum toxicity in the chicken embryo

Microliter amounts of South Louisiana crude oil (SLCO) or Prudhoe Bay crude oil (PBCO) were applied to the shell of fertile leghorn chicken eggs on day 8, 8.5 or 9 of incubation. Percent mortality and prevalence of grossly visible lesions were evaluated 96 h after treatment. The 96-h LD50s of SLCO at 8, 8.5 and 9 d of incubation were 2.6, 4.3 and 34.3 μl, respectively. Five μl PBCO caused nearly 100% mortality in 8 and 8.5-d-old embryos, while 12 μl caused 32% mortality in 9-d-old embryos. Liver necrosis, edema and increases in body weight and in the ratio of body weight to crown-rump length were found in embryos treated on day 8, 8.5 or 9 of incubation with either SLCO or PBCO. The 16-fold decrease in sensitivity of the embryo from day 8 to day 9 of incubation suggests that the chorioallantoic membrane may be important in the toxic action of petroleum oil.
Communicative ethnocide and Alevi television in the Turkish context

The attempted coup in Turkey in July 2016 provided a justification for the Turkish government to silence oppositional voices in the media and close down many television stations. Though the stated aim was to clamp down on the pro-coup Gulenist movement, the closure of TV channels has resulted in what I call a ‘communicative ethnocide’ silencing Alevi television in particular. Following Yalcinkaya, who builds on Clastres concept of ethnocide, I define ‘communicative ethnocide’ as the annihilation of the communicative capacity of a particular community by the state with the aim of destroying that community’s cultural identity. Although the closure of TV stations was not confined to Alevi channels, it has particular implications for the Alevi community by destroying its communicative capacity, infrastructure, relations with the viewers, and representation regime which are driven by the community’s political ambitions and attempts to sustain transnational connections. Parallels are drawn between Alevi and Kurdish TV to illustrate the Turkish context.
Andricus breviramuli Pujade-Villar n. sp. (Hymenoptera: Cynipidae: Cynipini): New Pest of Oaks in Mexico

Abstract. A new species of oak gall wasp, Andricus breviramuli Pujade-Villar n. sp. , is described from Mexico. The species is known only from asexual females. Data on the diagnosis, distribution, and biology of the new species are given. The wasp induces galls on twigs and young shoots of Quercus laeta Liebm. This gall wasp seems to be a serious pest of Q. laeta in Santa Fe (Delegación Cuajimalpa, DF), México City.
Effect of long term feeding of T-2 and HT-2 toxin contaminated diet on the glutathione redox status and lipid peroxidation processes in common carp (Cyprinus carpio L.)

Effect of sublethal T-2 (2.45 mg kg -1 feed) and HT-2 (0.52 mg kg -1 feed) toxin treatment for 4 weeks was investigated in common carp. Two groups, a control and a T-2+HT-2 toxin treated were formed. Six carps were exterminated from each group weekly. Liver samples were taken, in which reduced glutathione concentration and glutathione-peroxidase activity were measured. Free radical formation was measured by a direct reactive oxygen metabolites test, and also malondialdehyde concentration was determined. From the first week lower feed consumption and weight gain was recorded in T-2 toxin treated group, which resulted signifi- cantly lower live weight at the end of experiment. Feeding the T-2 toxin contaminated diet caused, significantly elevated glutathione concentration and glutathione-peroxidase activity during the first week. At second week the T-2 toxin loading resulted decrease in glutathione concentration and glutathione-peroxidase activity of liver as compared to the control. Although the reactive oxygen metabolite concentration was elevated in T-2 toxin treated group during the first two weeks, no significant changes were found in the MDA concentration. The results show that the biological antioxidant system was able to eliminate the harmful peroxidative effect of T-2 toxin in common carp.
Characterization of Matrix Metalloproteinase Expression in Triglyceride Treated THP-1 Macrophages

Elevated blood triglyceride (TG) levels correlate with development of atherosclerosis suggesting that TG may promote the development of this disease. During atherosclerosis, TG is taken up by tissue macrophages which result in dramatic changes in various secreted factors. One such factor is the family of matrix metalloproteases (MMP) which are involved in tissue remodeling during both physiological and pathological processes. In this study, we examined the MMP expression profile in PMA-differentiated THP-1 macrophages treated with TG. We found that TG-treated THP-1 macrophages showed decreased expression of MMP-3, MMP-7, MMP-8 and MMP-9 in a time- and dose-dependent manner. In contrast, expression of MMP-1, MMP-2, and MMP-10 remained relatively unchanged after TG treatment. In addition, we found that expression of select MMPs was affected by various inhibitors of signaling pathways. In particular, expression of MMP-3 was slightly recovered by cRAF and PLC signaling pathway inhibitors. These data suggests a possible role of MMPs in macrophages during TG-induced atherosclerosis.
Label-free proteomics reveals serum proteins whose levels differ between pancreatic ductal adenocarcinoma patients with short or long survival

Pancreatic ductal adenocarcinoma is the most common and aggressive type of pancreatic cancer, with a 5-year survival rate that is less than 10%. New biomarkers to aid in predicting the prognosis of pancreatic ductal adenocarcinoma patients are needed. Previous proteomic studies have to a great extent focused on finding proteins of value for the diagnosis of pancreatic ductal adenocarcinoma. There is a lack of studies that have profiled the serum or plasma proteome in order to discover candidates for new prognostic biomarkers. In this study, we have used ultra-performance liquid chromatography–ultra-definition mass spectrometry to analyze the serum samples of 21 pancreatic ductal adenocarcinoma patients with short or long survival. Statistical analysis discovered 31 proteins whose expression differed significantly between pancreatic ductal adenocarcinoma patients with short or long survival. Pathway analysis discovered multiple canonical pathways enriched in this data set, with several pathways having roles in inflammation and lipid metabolism. The serum proteins identified here, which include complement components and several enzymes, could be of value as candidates for new noninvasive prognostic markers.
Genetic Variability, Heritability and Genetic Advance in Muskmelon (Cucumis Melo Linn.)

Development of a variety needs exact information on genetic variability and heritability among the available accessions. Estimation of variation in a population is an effective tool for the breeder to design the testing procedures in order to identify superior genotypes. Genetic variability in a population is a result of genetic and environmental factors. To apportion the observed variability of these two factors, parameters such as genotypic and phenotypic coefficients of variation (GCV and PCV) have to be assessed. Heritability is another index for calculating the influence of environment on the expression of the genotype. Burton (1952) suggested that GCV together with heritability estimates would give best picture about the extent of advance to be expected by selection. Muskmelon is an unexploited vegetable crop and very less breeding programmes have been used to exploit available genetic variability. Therefore, an attempt was made to gather information on extent of variability, heritability and genetic advance for twelve quantitative characters in 44 diverge genotypes of muskmelon.
The Feasibility and Utility of a Personal Health Record for Persons With Dementia and Their Family Caregivers for Web-Based Care Coordination: Mixed Methods Study

Background Managing the complex and long-term care needs of persons living with Alzheimer disease and related dementias (ADRD) can adversely impact the health of informal caregivers and their care recipients. Web-based personal health records (PHRs) are one way to potentially alleviate a caregiver’s burden by simplifying ADRD health care management Objective This study aimed to evaluate Personal Health Record for Persons with Dementia and Their Family Caregivers (PHR-ADRD), a free web-based information exchange tool, using a multiphase mixed methods approach. Methods Dementia caregivers (N=34) were surveyed for their well-being and perceptions of PHR-ADRD feasibility and utility at 6 and 12 months using close- and open-ended questions as well as a semistructured interview (n=8). Exploratory analyses compared participants’ characteristics as well as PHR-ADRD use and experiences based on overall favorability status. Results Feasibility and utility scores decreased over time, but a subset of participants indicated that the system was helpful. Quantitative comparisons could not explain why some participants indicated favorable, neutral, or unfavorable views of the system overall or had not engaged with PHR-ADRD. Qualitative findings suggested that technology literacy and primary care provider buy-in were barriers. Both qualitative and qualitative findings indicated that time constraints to learn and use the system affected most participants. Conclusions Development and dissemination of PHRs for family caregivers of persons with ADRD should aim to make systems user-friendly for persons with limited time and technological literacy. Establishing health care provider buy-in may be essential to the future success of any PHR system.
Multiple regulatory layers in the establishment of Rbfox2 splicing networks

Regulated alternative splicing is mediated by RNA binding proteins (RBPs) recognizing short sequence motifs in nascent transcripts. The Rbfox RBPs are highly conserved splicing factors that regulate tissue-specific exon inclusion by binding the RNA motif UGCAUG. We sought to comprehensively define the Rbfox2 splicing regulatory network and discover determinants of Rbfox2 regulation in mouse embryonic stem cells. We uncovered fundamental principles in the mechanistic aspects of Rbfox-dependent splicing and in the systems-level regulation of interconnected splicing networks. Using high-resolution iCLIP and RNAseq, we identified many Rbfox2-mediated proteincoding splicing events and nearly 300 additional events, in particular those within RBPs, that are coupled to nonsense-mediated mRNA decay (NMD). Regulation of NMD-coupled splicing by Rbfox2 alters gene expression of autoregulated RBPs and hundreds of additional genes. These observations place Rbfox2 upstream of a large network of direct and indirect splicing changes and offer an explanation as to how autoregulated gene expression can be modulated. We describe a validation of RNA Bind-n-Seq, a novel in vitro technique for analyzing RNA-protein interactions. We found a secondary Rbfox2 motif, GCACG, to be functional in splicing regulation in addition to the consensus UGCAUG and observed a preference for Rbfox2 binding to unstructured sequences. These findings provide a foundation for establishing the critical determinants of functional cis elements in splicing regulation. We also investigated mechanisms of co-transcriptional splicing regulation by Rbfox2. Using chromatin immunoprecipitation, we found that Rbfox2 is recruited early in the transcription cycle to active promoters and transcriptional enhancers, likely via interaction and co-transcriptional tracking with RNA polymerase II. Modulation of chromatin structure alters Rbfox2-dependent splicing activity, supporting the emerging model that the chromatin environment influences exon choice. Our analyses of Rbfox2 activity in mouse embryonic stem cells reveal hundreds of previously unknown splicing targets involved in diverse biological functions. In particular, we introduce a novel concept in splicing regulation whereby changes in the expression of one splicing factor induce a cascade of secondary and perhaps tertiary splicing changes through cross-regulation of RBPs. This model positions RBPs at a critical node in the establishment, reinforcement, and alteration of tissue transcriptomes during mammalian development. Thesis supervisor: Phillip A. Sharp, Institute Professor of Biology
Photoperiodic induction without light-mediated circadian entrainment in a High Arctic resident bird

ABSTRACT Organisms use changes in photoperiod to anticipate and exploit favourable conditions in a seasonal environment. While species living at temperate latitudes receive day length information as a year-round input, species living in the Arctic may spend as much as two-thirds of the year without experiencing dawn or dusk. This suggests that specialised mechanisms may be required to maintain seasonal synchrony in polar regions. Svalbard ptarmigan (Lagopus muta hyperborea) are resident at 74–81°N latitude. They spend winter in constant darkness (DD) and summer in constant light (LL); extreme photoperiodic conditions under which they do not display overt circadian rhythms. Here, we explored how Arctic adaptation in circadian biology affects photoperiodic time measurement in captive Svalbard ptarmigan. For this purpose, DD-adapted birds, showing no circadian behaviour, either remained in prolonged DD, were transferred into a simulated natural photoperiod (SNP) or were transferred directly into LL. Birds transferred from DD to LL exhibited a strong photoperiodic response in terms of activation of the hypothalamic thyrotropin-mediated photoperiodic response pathway. This was assayed through expression of the Eya3, Tshβ and deiodinase genes, as well as gonadal development. While transfer to SNP established synchronous diurnal activity patterns, activity in birds transferred from DD to LL showed no evidence of circadian rhythmicity. These data show that the Svalbard ptarmigan does not require circadian entrainment to develop a photoperiodic response involving conserved molecular elements found in temperate species. Further studies are required to define how exactly Arctic adaptation modifies seasonal timer mechanisms. Summary: Svalbard ptarmigan show photoperiodic responses when transferred from constant darkness to constant light without circadian entrainment.