Miracle-dz/UniFAR-FTUs huggingface dataset:
Ion currents associated with root tips, emerging laterals and induced wound sites in Nicotians tabacum: spatial relationship proposed between resulting electrical fields and phytophthoran zoospore infection

Abstract Growing roots of Nicotiana tabacum var. Havana generate transcellular ion currents which traverse developing and wounded tissues. Positive current of around 10 mA m−2 enters meristematic and elongating cells at the tip of primary roots. The growing tips of first order laterals are also traversed by a similar positive current with a density of around 2.0 mA m−2, as are immature laterals emerging at the primary root surface. These self-generated ion currents flow basipetally through developing tissues and leave from mature non-elongating tissue. A large positive current of around 70 mA m−2 also enters induced wound sites on the primary root surface. Motile zoospores of the fungal pathogen Phytophthora parasitica var. nicotianae have been reported to associate preferentially with these regions of the root. This might suggest that electrotaxis may be part of the mechanism by which zoospores locate root regions susceptable to fungal infection.
Demographic variation and range contraction in the northern quoll, Dasyurus hallucatus (MArsupialia : Dasyuridae).

Mark-recapture studies of northern quoll (Dasyurus hallucatus) were conducted in lowland savanna in Kakadu National Park during two periods: in 1985-87 when total mammal abundance was high, and in 1989-91 when total mammal abundance was low. Population characteristics from these studies are compared with results from a 1977-79 study in sandstone escarpment country 40 km to the south-east and from studies in a range of habitats on the Mitchell Plateau in the Kimberley. Populations in rocky country are most dense with animals often surviving two or three years. In contrast, populations in savanna are more sparse, with males and females rarely surviving beyond one mating season. While all populations seem to undergo an annual period of stress, it is the savanna populations that seem most vulnerable. An analysis of the distribution of northern quolls shows a 75% recent range reduction, from being widespread over much of northern Australia to six smaller rocky regions. Possible causes of the decline include cattle, cane toads and exotic disease.
Genome-wide mapping of DNA-protein interactions in eukaryotes

Dedication I dedicate this work to My wife, Sumi, who has been with me since I met her at my old school seven years ago, and To my parents and parents-in-law who have always supported me in everything I did. Their love and encouragement has kept me working on my research. v Acknowledgements First and foremost, I would like to thank my supervisor, Dr. Vishwanath Iyer for his patience, encouragement, and mentorship that he has provided me during my work in his laboratory. He has given me many important lessons about being a good scientist, the most important being patience, steadiness, and thoroughness in overcoming obstacles. I would like to thank the former and present members of the Iyer lab for their assistance. Without their help, I would have never printed a single yeast or human microarray. I would like to thank Sushma, and Bumkyu for their helpful discussions and advices during my years in the lab. I would especially like to thank Akshay for assistance in the analysis of STAGE data during days and nights in the computer room. I would like to thank my friends who are studying biology at UT and other places for showing me their enthusiasm and passion for science as junior researchers-with them always made me more focused on science. me to the way of science. Finally, I would like to thank my wife Sumi, who has supported me in everything from raising my little boy to helping me to concentrate on my work, and additionally my little son Hyun, who made my life more happy and meaningful. The genome of an organism encodes thousands of genes, and their expression needs to be precisely controlled at the right place and time for normal cellular functioning. Control of gene expression occurs predominantly at the level of transcription and the transcription of a particular gene is determined by the interactions between diverse regulatory proteins and their specific cis-acting binding elements. However, our understanding about how and when transcription factors function in the context of the whole genome is limited. Hundreds to thousands of transcription factors can potentially interact with DNA in the genome and modulate the level of transcription of protein coding genes into mRNAs in response to regulatory signals. Identifying the chromosomal targets of regulatory transcription factors in various conditions is crucial for reconstructing the transcriptional regulatory networks underlying global gene expression programs. Recently-developed chromatin …
Osteology of Bufo sternosignatus Günther, 1858 (Anura: Bufonidae) with Comments on Phylogenetic Implications

Abstract Osteological characters are used to infer the phylogenetic relationships of the Venezuelan toad, Bufo sternosignatus. The species does not have a ventrolateral process on the quadratojugal, a synapomorphy for the especies of the B. typhonius clade and is associated to B. humboldti a species of the B. granulosus group.
Chromatin Structure and Transcriptional Regulation of the β-Globin Locus

Chromatin structure plays a critical role in eukaryotic gene transcriptional regulation. The β-globin locus provides an ideal system within which to study the interplay between chromatin structure and transcriptional regulation. The process of β-globin locus activation is remarkably intricate and involves at least two distinct events: chromatin opening and gene activation. Great progress has been made in recent years in understanding how locus control regions confer high-level expression to linked genes. Current interest focuses on some special events, including formation of locus control region hypersensitivity sites, ATP-dependent chromatin remodeling, localized H3 hyperacetylation, and intergenic transcription, which link chromatin and β-globin locus regulation. These events, and their possible molecular bases, are summarized together with speculations concerning their connections.
Meeting Report: Signaling Schemes for TGF-β

The transforming growth factor-β (TGF-β) superfamily of signaling molecules regulates many developmental processes in a range of organisms from worms to humans. Understanding the mechanisms by which they exert their repertoire of effects has required identification of the components of signaling pathways that they control. Roberts and Derynck focus on this aspect of TGF-β biology in their review of a recent Federation of American Societies for Experimental Biology (FASEB) meeting on TGF-β signaling and development and summarize current signaling paradigms and future prospects in TGF-β signaling from the cell surface to the nucleus.
How to Model Electromagnetic Problems Without Using Vector Calculus and Differential Equations?

ABSTRACT Two important mathematical tools, namely, vector calculus and differential equations dominate the domain of computational electromagnetics. These two tools, though powerful, are not always needed for practical modelling of electromagnetic problems. In this paper, we are presenting an alternative approach using algebraic topology. We discuss some of the important advantages of this approach over other mainstream methods and highlight opportunities and directions for future research.
Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy: New beamlines and new applications in biology

New advances in instrumentation, demonstration of proof-of-principle studies, and development of new tools and methods for data analysis and interpretation have enabled the technique of Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy to become a useful tool for structural and functional biology. This paper discusses the characterisation of two new SRCD beamlines, CD1 at the Institute for Storage Rings (ISA), Denmark and 4B8 at the Beijing Synchrotron Radiation Facility (BSRF), China, and new applications of the method for examining biological systems.
Osmundea lata (M. Howe & W.R. Taylor) comb. nov. (Ceramiales, Rhodophyta) from the Brazilian south-eastern continental shelf

Abstract Specimens of Laurencia lata were dredged from the south-eastern Brazilian continental shelf near Cabo Frio (off the state of Rio de Janeiro) from a depth of 60 m, growing as epiphytes on the rhizoids of Laminaria abyssalis. Detailed examination of the vegetative and reproductive morphology of these specimens revealed anatomical characteristics belonging to the recently resurrected genus Osmundea. Such features include two periaxial cells per vegetative axial segment, spermatangial branches arising directly from apical and epidermal cells in the apical pit of branchlets (filament type), and tetrasporangia cut off from random epidermal cells. On the basis of these features, Osmundea lata (M. Howe & W.R. Taylor) Yoneshigue-Valentin, M.T. Fujii & Gurgel is proposed as a new combination for Laurencia lata. We present detailed observations of the vegetative and reproductive morphology of O. lata, and compare it with related species; its geographical distribution is also discussed.
Laboratory and Field Evidence for Structural Habitat Affinity of Young‐of‐the‐Year Lingcod

Abstract Lingcod Ophiodon elongatus are an overexploited fisheries species in the Pacific Northwest. Although there has been extensive study of the habitat requirements of adults, particularly during spawning, relatively little is known about the habitat requirements of juveniles. Many juvenile fish use structural components of habitat to alleviate the risk of predation as well as for foraging. Laboratory experiments and a field tagging study were performed to investigate habitat preference in juvenile lingcod. Initial laboratory experiments demonstrated an affinity for structure (rock, shell, or seagrass) over bare sand habitats. An acoustic tagging study conducted in Yaquina Bay, Oregon, corroborated the basic habitat preferences seen in laboratory experiments. Juvenile lingcod showed a high degree of site fidelity, remaining in discreet areas of significant structural complexity, as evidenced by underwater video of benthic habitat. Results from both laboratory and field studies establish that juvenile .
Primeiro registro de Trypanosoma vivax em bovinos no Estado do Rio Grande do Sul, Brasil

This study aimed at reporting the occurrence of Trypanosoma vivax in southern Brazil. The protozoan was diagnosed through peripheral blood smear evaluation of a bovine and confirmed by the evaluation of the trypomastigote forms morphology and by the Polimerase Chain Reaction (PCR). The animal showed clinical signs similar to the nervous form of the infection by T. vivax. Negative results for T. vivax were found in other bovines grazing in the same paddock. This is the first report of T. vivax in the state of Rio Grande do Sul and in the southern region of Brazil.
Expression of Potato Virus X Resistance Gene Rx in Potato Leaf Protoplasts

Summary Protoplasts derived from shoot cultures of potato cv. Cara, which carries immunity gene Rx, supported only limited virus multiplication after inoculation with particles or RNA of isolate DX, a group 3 strain of potato virus X, as compared to similarly inoculated protoplasts of cultivars King Edward and Pentland Ivory which lack Rx. The Cara protoplasts were, however, able to support extensive replication of the resistance-breaking strain HB. This strain-specific resistance did not appear to be mediated by a failure or inhibition of the uncoating mechanism or of virus assembly.
Limited Response of Indigenous Microbes to Water and Nutrient Pulses in High-Elevation Atacama Soils: Implications for the Cold–Dry Limits of Life on Earth

Soils on the world’s highest volcanoes in the Atacama region represent some of the harshest ecosystems yet discovered on Earth. Life in these environments must cope with high UV flux, extreme diurnal freeze–thaw cycles, low atmospheric pressure and extremely low nutrient and water availability. Only a limited spectrum of bacterial and fungal lineages seems to have overcome the harshness of this environment and may have evolved the ability to function in situ. However, these communities may lay dormant for most of the time and spring to life only when enough water and nutrients become available during occasional snowfalls and aeolian depositions. We applied water and nutrients to high-elevation soils (5100 meters above sea level) from Volcán Llullaillaco, both in lab microcosms and in the field, to investigate how microbial communities respond when resource limitations are alleviated. The dominant taxon in these soils, the extremophilic yeast Naganishia sp. , increased in relative sequence abundance and colony-forming unit counts after water + nutrient additions in microcosms, and marginally in the field after only 6 days. Among bacteria, only a Noviherbaspirillum sp. (Oxalobacteraceae) significantly increased in relative abundance both in the lab and field in response to water addition but not in response to water and nutrients together, indicating that it might be an oligotroph uniquely suited to this extreme environment. The community structure of both bacteria and eukaryotes changed significantly with water and water + nutrient additions in the microcosms and taxonomic richness declined with amendments to water and nutrients. These results indicate that only a fraction of the detected community is able to become active when water and nutrients limitations are alleviated in lab microcosms, and that water alone can dramatically change community structure. Our study sheds light on which extremophilic organisms are likely to respond when favorable conditions occur in extreme earthly environments and perhaps in extraterrestrial environments as well.
The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health

The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture‐animal‐manure‐soil‐water‐plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic‐resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro‐ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro‐ecosystem; and possible ways to curtail the menace of antimicrobial resistance.
Investigation of the Environmental and Socio-Economic Characteristics of Counties with a High Asthma Burden to Focus Asthma Action in Utah

Rising adult asthma prevalence (AAP) rates and asthma emergency room (AER) visits constitute a large burden on public health in Utah (UT), a high-altitude state in the Great Basin Desert, USA. This warrants an investigation of the characteristics of the counties with the highest asthma burden within UT to improve allocation of health resources and for planning. The relations between several predictor environmental, health behavior and socio-economic variables and two health outcome variables, AAP and AER visits, were investigated for UT’s 29 counties. Non-parametric statistical comparison tests, correlation and linear regression analysis were used to determine the factors significantly associated with AER visits and AAP. Regression kriging with Utah small area data (USAD) as well as socio-economic and pollution data enabled local Moran’s I cluster analysis and the investigation of moving correlations between health outcomes and risk factors. Results showed the importance of desert/mining dust and socio-economic status as AAP and AER visits were greatest in the south of the state, highlighting a marked north–south divide in terms of these factors within the state. USAD investigations also showed marked differences in pollution and socio-economic status associated with AAP within the most populous northern counties. Policies and interventions need to address socio-economic inequalities within counties and between the north and south of the state. Fine (PM2.5) and coarse (PM10) particulate matter monitors should be installed in towns in central and southern UT to monitor air quality as these are sparse, but in the summer, air quality can be worse here. Further research into spatiotemporal variation in air quality within UT is needed to inform public health interventions such as expanding clean fuel programs and targeted land-use policies. Efforts are also needed to examine barriers to routine asthma care.
MicroRNAs from Liquid Biopsy Derived Extracellular Vesicles: Recent Advances in Detection and Characterization Methods

Liquid biopsies have become a convenient tool in cancer diagnostics, real-time disease monitoring, and evaluation of residual disease. Yet, the information still encrypted in the variety of tumor-derived molecules identified in biofluids has proven difficult to decipher due to the technological limitations imposed by their biological nature. Such is the case of extracellular vesicle (EV) encapsulated ncRNAs, which have gained traction in recent years as biomarkers. Due to their resilience towards degrading factors they may act as suitable disease indicators. This review addresses the less described issues in this context. We present an overview of less investigated biofluids that can be used for EV isolation in addition to different isolation approaches to overcome the technical challenges these specimens harbor. Furthermore, we summarize the latest technological advances providing improvement to ncRNA detection and analysis. Thereby, this review summarizes the current state-of-the-art methodologies regarding EV and EV derived miRNA analysis and how they compare to current approaches.
Biomarkers of Browning in Cold Exposed Siberian Adults

Cold-exposure promotes energy expenditure by inducing brown adipose tissue (BAT) thermogenesis, which over time, is also sustained by browning, the appearance, or increase, of brown-like cells into white fat depots. Identification of circulating markers reflecting BAT activity and browning is crucial to study this phenomenon and its triggers, also holding possible implications for the therapy of obesity and metabolic diseases. Using RT-qPCR, we evaluated the peripheral blood mononuclear cells (PBMC) expression profile of regulators of BAT activity (CIDEA, PRDM16), white adipocytes browning (HOXC9 and SLC27A1), and fatty acid β-oxidation (CPT1A) in 150 Siberian healthy miners living at extremely cold temperatures compared to 29 healthy subjects living in thermoneutral conditions. Anthropometric parameters, glucose, and lipid profiles were also assessed. The cold-exposed group showed significantly lower weight, BMI, hip circumference, and PBMC expression of CIDEA, but higher expression of HOXC9 and higher circulating glucose compared to controls. Within the cold-exposed group, BMI, total cholesterol, and the atherogenic coefficient were lower in individuals exposed to low temperatures for a longer time. In conclusion, human PBMC expresses the brown adipocytes marker CIDEA and the browning marker HOXC9, which, varying according to cold-exposure, possibly reflect changes in BAT activation and white fat browning.
A prospective randomized controlled trial comparing laparoscopic versus open Whipple’s procedure for periampullary malignancy

Background: Laparoscopic surgery in cases of periampullary region malignancies has been emerging as a preferable alternative to open pancreatoduodenectomy due to their benefits such as early mobilization and shorter duration of hospital stay. We conducted this study to determine whether laparoscopic approach is comparable to open pancreatoduodenectomy in terms of hospital stay, blood loss, complications, pathological radicality with oncological safety and overall postoperative short-term outcomes.Methods: This was a single-center, non-stratified, balanced allocation, open-label, parallel-group randomized control study in which patients who had undergone Whipple’s procedure were included. Patients were randomized after confirmation of non-metastatic status into either the laparoscopy (N=15) or open surgery group (N=15). The primary outcome variable was duration of postoperative hospital stays. Secondary outcomes were duration of surgery, blood loss, complication rates (using definitions of the international study group of pancreatic surgery) and pathological radicality of resection.Results: Pain in abdomen was the predominant complaint which was seen in 12 (80%) and 10 (66%) patients each. The other common symptoms were weight loss, vomiting and jaundice. Surgical site infection, mean blood loss and mean operative duration was significantly lower in laparoscopic group (P<0.05). Mean tumor size was more in open group. Mortality was comparable in both the groups.Conclusions: Laparoscopic pancreatoduodenectomy offers significant benefit in terms of hospital stay, surgical site infection, mean blood loss, mean operative duration and mean interval of duration receiving chemo/radiotherapy as compared to open surgery in cases of periampullary region malignancy.
Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle

Aging is a biological phenomenon common to all living organisms. It is thought that the rate of aging is influenced by diverse factors, in many cases related to the control of energy metabolism, i.e., the so-called pro-longevity effects of starvation. Translation, regarded as the main energy consumption process, lies at the center of interest, as it has a significant impact on the longevity phenomenon. It has been shown that perturbations in the translational apparatus may lead to a lower rate of aging. Therefore, the main aim of this study was to investigate aging in relation to the protein biosynthesis circuit, taking into account the uL11 ribosomal protein as a vital ribosomal element. To this end, we used set of yeast mutants with deleted single uL11A or uL11B genes and a double disruptant uL11AB mutant. We applied an integrated approach analyzing a broad range of biological parameters of yeast mutant cells, especially the longevity phenomenon, supplemented with biochemical and high throughput transcriptomic and metobolomic approaches. The analysis showed that the longevity phenomenon is not fully related to the commonly considered energy restriction effect, thus the slow-down of translation does not represent the sole source of aging. Additionally, we showed that uL11 can be classified as a moonlighting protein with extra-ribosomal function having cell-cycle regulatory potential.