Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant Functional Traits Predict the Drought Response of Native California Plant Species

Premise of research. As extreme climate events, such as California’s 2012–2016 drought, become more frequent with climate change, it is imperative to understand how different native plant communities respond to drought-induced dehydration stress. Chaparral and California sage scrub (CSS), two widespread plant communities in California, face threats from droughts of increased frequency and severity. Despite chaparral and CSS plants being adapted to seasonal drought conditions, it is not known how the strategies of recovery from extreme multiyear droughts associated with changing climate differ between them. Methodology. We measured chlorophyll fluorescence and water potentials for two evergreen chaparral shrubs (Heteromeles arbutifolia and Quercus berberidifolia) and two drought deciduous CSS shrubs (Salvia leucophylla and Salvia mellifera) in the Santa Monica Mountains both during and after the extreme drought in California (between 2015 and 2017). Pivotal results. We found that the maximum electron transport rate (Jmax) varied seasonally for all species, decreasing in the dry season and recovering in the wet season. However, Jmax and the seasonal change in Jmax (ΔJmax) were larger for the CSS species than for the chaparral species, and recovery of Jmax began earlier in the year for CSS species than for chaparral species. Dark-adapted maximum photochemical efficiency of photosystem II (Fv/Fm) and both midday (ΨMD) and predawn (ΨPD) water potential for all species also followed similar seasonal patterns—higher in the wet season than in the dry season, with CSS species exhibiting the largest seasonal changes in Ψ. A strong linear relationship was found between Jmax and ΨMD for all species except Q. berberidifolia. Conclusions. Our results show that recovery from drought-induced dehydration differs between representatives of two major plant communities in California and is linked to life-history strategy: the higher sensitivity to and quicker recovery from seasonal drought for the CSS species compared with the chaparral species could be attributed to the shallower rooting depths and dehydration tolerance of the CSS species. In addition, water relations and chlorophyll fluorescence can serve as useful metrics to compare species-specific dehydration stress tolerance or avoidance strategies in the field.
Performance appraisal of administrative staff in a Tertiary Institution: perception

There is little empirical evidence relating to how university administrative employees view the performance appraisal process (Analoui & Fell, 2002). The aim of this paper was to investigate administrative staff perceptions and understanding of the appraisal system using AUT University (AUT) as a case study. Areas investigated included (1) how administrative staff viewed the process, (2) did it impact on their motivation, and (3) did it help or hinder career development. The research for this paper was a partial replication of the Analoui and Fell study of appraisal systems at The University of Bradford (UK). The Analoui and Fell questionnaire and interview guide were modified to suit the AUT context. The AUT sample consisted of 543 staff members with a response rate of 20 per cent. It was found that there was no evidence that the respondents wanted the process discontinued even though comments from those who had been through a Performance and Development Review (P&DR) and Formative Appraisal (FA) indicated a range of positive and negative experiences. In terms of performance appraisal as a motivational tool, few respondents felt that the process motivated them. There was evidence that FA was beneficial in helping with career development. The stated main purposes of AUT performance appraisal is: to assist in administration (pay increase and promotion), and developmental (training) decisions, with the latter purpose being secondary. Resulting from this study recommendations are (1) the current process should be evaluated, and (2) appraisers and appraisees should undertake training prior to an appraisal. On-going research should be undertaken to find out how administrative staff in the wider NZ university sector view the process. To follow-on from the current research, a longitudinal study should be undertaken of administrative staff reactions immediately after an appraisal. Research should also be undertaken to investigate if administrative staff associate completion of the performance appraisal process which includes the setting of goals with an increased work overload.
Anti-p53 antibodies in colorectal cancer patients

Introduction . The aim of the study was to determine the association between anti-p53 antibodies, serum CEA levels and the immunohistochemically assessed accumulation of the p53 protein in the nuclei of tumor cells in selected patients with colorectal cancer and histological tumor stage according to Astler-Coller, tumor localization and size, the degree of histological differentiation and histological type, metastatic disease involving the peri-intestinal lymph nodes and patient gender and age. Material and methods . The study included 229 patients with colorectal cancer diagnosed on the basis of histo- pathological or cytological examinations. In all the patients, serologic examinations were performed (serum anti-p53 antibodies presence and serum CEA level), in 221 patients, tumor tissue was available for histopathological examination. Results . Serum anti-p53 antibodies were found in 62 patients (27%) with stage D disease according to Astler-Coller, p53 protein antibodies were more frequent in this group than in stage B2 patients (p=0.02). Serum anti-p53 antibodies were also more frequent in patients with tumors located in the descending colon, as compared to the ascending colon (p=0.04). In patients with tumors with a diameter of more than 25 mm or 30 mm, serum anti-p53 antibodies were more frequent than in patients with tumor less than or equal to 25 mm or 30 mm in diameter. The percentage of tumors with p53 protein accumulation was higher in stage B1 than in stage C2 (p=0.02), similarly as in the sigmoid vs. the ascending colon (p=0.01), in the rectum vs. the ascending colon (p=0.01) and in the left colon vs. the right colon (p=0.003). Conclusions . 1.The presence of anti-p53 antibodies in the serum of patients with colorectal cancer depends on the size, location and tumor stage according to Astler-Coller. 2.The presence of serum anti-p53 antibodies in 25% of colorectal cancer patients only limits the use of the antibodies in clinical practice, for example as a a prognostic factor, or in postoperative monitoring.
AP-1B facilitates endocytosis during cell migration

The epithelial cell-specific clathrin adaptor AP-1B has a well-established role in polarized sorting of cargos to the basolateral membrane. Here we demonstrate a novel function for AP-1B during collective cell migration of epithelial sheets. We show that AP-1B colocalized with β1 integrin in focal adhesions during cell migration using confocal microscopy and total internal reflection fluorescence (TIRF) microscopy on fixed specimens. Further, AP-1B labeling in cell protrusion was distinct from labeling for the canonical endocytic adaptor complex AP-2. Using stochastic optical reconstruction microscopy (STORM) and live TIRF imaging we identified numerous AP-1B-coated structures at or close to the plasma membrane in cell protrusions. Importantly, immuno-electron microscopy (EM) showed AP-1B in clathrin-coated pits and budding vesicles at the plasma membrane during cell migration. Our data therefore established a novel function for AP-1B in endocytosis. We further show that β1 integrin was dependent on AP-1B and its co-adaptor, autosomal recessive hypercholesterolemia protein (ARH), for sorting to the basolateral membrane. Notably, we found that expression of AP-1B (and ARH) slowed epithelial-cell migration, and qRT-PCR analysis of human epithelial-derived cell lines revealed a loss of AP-1B expression in highly metastatic cancer cells indicating that AP-1B-facilitated endocytosis during cell migration might be an anti-cancer mechanism.
Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”

Background The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In S. cerevisiae, a preinitiation complex comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. Results To determine extent of promoter scanning across promoter classes in S. cerevisiae, we perturbed Pol II catalytic activity and GTF function and analyzed their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. Conclusions Our observations coupled with previous data validate this scanning model for Pol II initiation in yeast – which we term the “shooting gallery”. In this model, Pol II catalytic activity, and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage. Comparison of TSS distributions and their relationship to promoter sequence among other eukaryotes suggest some, but not all, share characteristics of S. cerevisiae.
FORMULATION AND IN VITRO EVALUATION OF NIOSOMAL POVIDONE -IODINE CARRIERS AGAINST Candida albicans

Objective: Use of povidone-iodine (PVP-I) as a microbicidal agent is complicated by contact burns and other adverse reactions attributed to its sudden concentrated release from absorbent skin bandages. The current investigation examines the potential of niosomes or non–ionic surfactant vesicles to aid in the slow sustained release of the topical antiseptic in order to overcome this major drawback. Method: Candida albicans, a fungus commonly associated with cutaneous infections was selected as the test organism since PVP-I has broad spectrum properties and been reported to be an effective antimycotic agent. After evaluating the antimicrobial effect of unencapsulated PVP-I on Candida cells, niosomes were developed by the thin film hydration technique, with a stoichiometric proportion of antiseptic: cholesterol: sorbitane monooleate of 1:1:2. The formulated vesicles were characterized for their particle size, zeta potential and drug entrapment efficiency. Further, in vitro agar cup tests and studies on the sustained release profile of the entrapped medicament were performed. Results: The minimum inhibitory concentration of PVP-I for Candida was found to be 0.45% w/v available iodine and complete killing of cells was achieved at this concentration within 180 seconds. The average size of loaded vesicles was recorded to be 338.4 nm, with a drug entrapment efficiency of 80%. Subsequent to its encapsulation, PVP-I showed good permeability, retention of the fungicidal activity and the slow sustained effect lasted for almost 35 hours. Conclusion: This is the first report of a study that has developed and characterized the in vitro efficacy and sustained drug delivery of PVP-I using niosomal carriers. The results demonstrate that niosomes can act as microreservoirs prolonging the release of PVP-I. They could thus help to prevent contact burns associated with the immediate release of the antiseptic when used for topical application.
Microbiome and next generation sequencing

The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods. At present, metagenomic applies a suite of genomic technologies, where the microorganisms are identified by their genomic fingerprint. The 16S rRNA subunit is considered as the universal target for bacterial identification from DNA with the aid of sequencing. Sanger sequencing technology had a great impact on the first generation sequencing due to its simplicity and precision. Platforms high-throughput known as second generation secuencing technologies are capable to generate hundreds of thousands of sequence reactions in a faster and economic way. However, thanks to the third generation sequencing the greatest advances in nanotechnology have been made. Using the reference gene, the massive sequencing techniques and bioinformatics tools used for the data processing, there has been an important development of the human microbiome, achieving an unprecedented detail level on the taxonomy and microbial function. This has meant an authentic revolution not only in their knowledge but also in their involvement in the health or illness of the human being.
Comparative Collagen Distribution in the Small Intestine of Eidolon Helvum and Manis Tricuspis

The African tree pangolin has no teeth but consumes a highly tough and chitinous diet while the bat is frugivorous; this study was designed to compare the morphological adaptations of the small intestine of both mammals by investigating the collagen distribution and hydroxyproline/collagen content of their duodenum and ileum histologically and spectrophotometrically respectively. Ten animals each of both sexes were used. Portions of their small intestine were either fixed for routine histologic processing or homogenized and assayed for the hydroxyproline assay. Histological staining reveal that the collagenous distribution of duodenal submucosa and support of the villus core of the ileum is more prominent in the Pangolin than in the Bat. Data from the hydroxyproline colorimetric assay reveals that the Pangolin has significantly (p = 0.00042) higher total collagen content than in the Bat. It is concluded that the Pangolin has evolved a higher expression and distribution of collagen in their small intestine as a mechanism of coping with their tough diets despite the lack of teeth.
Optimal Design of Single-Cell Experiments within Temporally Fluctuating Environments

Modern biological experiments are becoming increasingly complex, and designing these experiments to yield the greatest possible quantitative insight is an open challenge. Increasingly, computational models of complex stochastic biological systems are being used to understand and predict biological behaviors or to infer biological parameters. Such quantitative analyses can also help to improve experiment designs for particular goals, such as to learn more about specific model mechanisms or to reduce prediction errors in certain situations. A classic approach to experiment design is to use the Fisher information matrix (FIM), which quantifies the expected information a particular experiment will reveal about model parameters. The Finite State Projection based FIM (FSP-FIM) was recently developed to compute the FIM for discrete stochastic gene regulatory systems, whose complex response distributions do not satisfy standard assumptions of Gaussian variations. In this work, we develop the FSP-FIM analysis for a stochastic model of stress response genes in S. cerevisae under time-varying MAPK induction. We validate this FSP-FIM analysis and use it to optimize the number of cells that should be quantified at particular times to learn as much as possible about the model parameters. We then demonstrate how the FSP-FIM approach can be extended to explore how different measurement times or genetic modifications can help to minimize uncertainty in the sensing of extracellular environments, such as external salinity modulations. This work demonstrates the potential of quantitative models to not only make sense of modern biological data sets, but to close the loop between quantitative modeling and experimental data collection.
Demography-Dispersal Trait Correlations Modify the Eco-Evolutionary Dynamics of Range Expansion

Spreading populations are subject to evolutionary processes acting on dispersal and reproduction that can increase invasion speed and variability. It is typically assumed that dispersal and demography traits evolve independently, but abundant evidence points to correlations between them that may be positive or negative and genetic, maternal, or environmental. We sought to understand how demography-dispersal correlations modify the eco-evolutionary dynamics of range expansion. We first explored this question with the beetle Callosobruchus maculatus, a laboratory model in which evolutionary acceleration of invasion has been demonstrated. We then built a simulation model to explore the role of trait correlations in this system and more generally. We found that positive correlations amplify the positive influence of evolution on speed and variability while negative correlations (such as we found empirically) constrain that influence. Strong negative genetic correlations can even cause evolution to decelerate invasion. Genetic and nongenetic (maternal and environmental) correlations had similar effects on some measures of invasion but different effects on others. Model results enabled us to retrospectively explain invasion dynamics and trait evolution in C. maculatus and may similarly aid the interpretation of other field and laboratory studies. Nonindependence of demography and dispersal is an important consideration for understanding and predicting outcomes of range expansion.
In Vitro Studies of the Synergy Between Mechanical Loading and Genetics Within Human Induced Pluripotent Stem Cell Derived Micro-Scale Engineered Heart Tissues

Introduction: Human induced pluripotent stem cell (iPSC) and genome editing technologies offer the promise of understanding the molecular basis of disease and developing personalized therapies. However, mechanical cues are important in disease pathophysiology, particularly in the heart. For example, sarcomere mutations and blood pressure are both major risk factors for heart disease. Tissue engineering approaches offer the potential to study tissue-specific effects of mechanical loading. In our studies, we used genome editing (TALEN and CRISPR/Cas9) to introduce defined loss-of-function mutations in proteins including the myosin binding protein C isoform 3 (MYBPC3) which are associated with cardiomyopathy. We then used highly polymer-based scaffolds with controlled resistance to cell contractile forces to induce self-assembly of heart muscle from iPSC-derived cardiomyocytes (iPS-CM). Although a complete loss of MYBPC3 should result in a very severe phenotype in the human heart, MYBPC3 null iPS-CM only exhibited defects in force when cultured on rigid scaffolds. This is consistent with observed contributions of both biophysical and genetic cues to cardiac disease progression and suggests that it is important to consider mechanical cues within in vitro disease models.
Comprehensive palmitoyl-proteomic analysis identifies distinct protein signatures for large and small cancer-derived extracellular vesicles

Extracellular vesicles (EVs) are membrane-enclosed particles that play an important role in cancer progression and have emerged as a promising source of circulating biomarkers. Protein S-acylation, also known as palmitoylation, has been proposed as a post-translational mechanism that modulates the dynamics of EV biogenesis and protein cargo sorting. However, technical challenges have limited large-scale profiling of the whole palmitoyl-proteins of EVs. We successfully employed a novel approach that combines low-background acyl-biotinyl exchange (LB-ABE) with label-free proteomics to analyze the palmitoyl proteome of large EVs (L-EVs) and small EVs (S-EVs) from prostate cancer cells. Here we report the first palmitoyl-protein signature of EVs, and demonstrate that L- and S-EVs harbor proteins associated with distinct biological processes and subcellular origin. We identified STEAP1, STEAP2, and ABBC4 as prostate cancer-specific palmitoyl proteins enriched in both EV populations in comparison with the originating cell lines. Importantly, the presence of the above proteins in EVs was significantly reduced upon inhibition of palmitoylation in the producing cells. These results suggest that palmitoylation may be involved in the differential sorting of proteins to distinct EV populations and allow for better detection of disease biomarkers.
Antioxidant, Antidiabetic, and Antihyperlipidemic Activities of Dolichandrone atrovirens in Albino Wistar rats

Aim: To investigate the antioxidant, antidiabetic, and antihyperlipidemic activities of Dolichandrone atrovirens in albino wistar rats. Methods and Material: Bark and leaf part of Dolichandrone atrovirens were extracted with water and methanol. Swiss albino wistar rats were used to evaluate the in vivo effects of streptozotocin induced body weight loss, oxidative stress, hyperglycemia and hyperlipidemia. Statistical analysis used: Data were analysed by One - way ANOVA, followed by Turkey –Kramer Multiple Comparison Test. Results: Dolichandrone atrovirens extract treated animals demonstrated significant increase in body weight, decreased blood glucose levels, glycosylated haemoglobin and changes in other biochemical parameters levels when compared to diabetic control rats.
Obesity Potentiates TH2 Immunopathology via Dysregulation of PPARγ

How obesity affects immune function is not well understood. Clinically, obesity is strongly associated with severe TH2 immunopathology1-3, though the physiological, cellular, and molecular underpinnings of this association remain obscure. Here, we demonstrate that obese mice are susceptible to severe atopic dermatitis (AD), a major manifestation of TH2 immunopathology and disease burden in humans4,5. Mechanistically, we show that dysregulation of the nuclear hormone receptor (NHR) PPARγ (peroxisome proliferator-activated receptor gamma) in T cells is a causal link between obesity and the increased TH2 immunopathology. We find that PPARγ oversees a cellular metabolic transcriptional program that restrains nuclear gene expression of the chief TH2 priming and effector cytokine interleukin-4 (IL-4). Accordingly, thiazolidinediones (TZDs), potent PPARγ agonists, robustly protect obese mice from TH2 immunopathology. Collectively, these findings establish PPARγ as a molecular link between obesity and TH2 immune homeostasis and identify TZDs as novel therapeutic candidates for TH2 immunopathology. Fundamentally, these findings demonstrate that shifting physiologic metabolic states can shape the tone of adaptive immune responses to modulate differential disease susceptibility.