Miracle-dz/UniFAR-FTUs huggingface dataset:
The identification of miRNA biomarkers of chronic kidney disease and development of minimally-invasive methods of molecular detection

Kidney biopsy is the current gold standard diagnostic test for intrinsic renal disease but requires hospital admission and carries a 3% risk of major complications. Current non-invasive prognostic indicators such as urine protein quantification have limited predictive value. Better diagnostic and prognostic tests for chronic kidney disease (CKD) patients are therefore a major focus for industry and academia. An alternative approach is the quantification of urinary microRNAs(miRNAs): short, non-coding RNAs that regulate gene expression posttranscriptionally. This project investigated the utility of urinary miRNA expression analysis as a method for non-invasive diagnostic/prognostic testing for CKD. A technique was developed for quantifying miRNAs in urine samples from control subjects and diabetic nephropathy (DN) patients with a coefficient of variation below 10%. The stability of endogenous miRNAs was demonstrated in urine samples from unaffected individuals and DN patients. Two populations of urinary miRNAs were identified: those associated with exosomes and those associated with AGO2, a component protein of the RNA-induced silencing complex. Expression of over 750 urinary miRNAs in pooled urine samples from DN patients was compared with that in corresponding control samples using TaqMan Array Human microRNA Card analysis. Statistically significant differences in expression of a subset of putative disease-associated miRNAs were then replicated in individual urine samples, and these data were supported by ROC curve analyses. Expression analysis of these target miRNAs in defined nephron segments was observed using laser capture microdissection of renal biopsy tissues followed by miRNA detection by RT-qPCR. Subsequent renal cell line analysis pinpointed miRNA cellular origins, and miRNA release into conditioned tissue culture medium in response to disease stimuli was also observed. These experimental data reveal a pattern of urinary miRNA expression changes in DN and present putative mechanisms by which these differences in abundance might come about.
Isolation, identification and biological characterization of Acanthamoeba polyphaga from suspected cases of eye patients and its electron microscopy.

Corneal scrapings and tear drop of 90 patients with suspected cases of keratitis and eye infection attending the Govt. Hospital and rural areas patients of Lucknow city were screened for amoebic pathogens including Acanthamoeba. Of these, 6 (6.66percent) were positive for Acanthamoeba, which fulfilled the criteria for suspecting Acanthamoeba keratitis. These were distributed among all ages with the maximum numbers in the 20-45 year age group. None of the patients were using contact lenses and were mostly agricultural labourers and had recent history of swimming in ponds and river and also associated with water sports. The predisposing factor found in this study was trauma of varying degrees. The result of present study confirmed that Amphizoic amoebae colonized almost every conceivable aquatic habitat. This is alarming signal that shows presence of Amphizoic amoebae. Incidences of infection during warm season have been traced in patients suffering from eye infection. Preventive measures include public awareness and maintenance of water body and adequate chlorination.
Genetics of Central Valley, O. mykiss, Populations: Drainage and Watershed-scale Analyses

Author(s): Nielsen, Jennifer L. ; Pavey, Scott A. ; Wiacek, Talia; Williams, Ian | Abstract: Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M l 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts.
A study of mitochondrial biogenesis in the rodent nervous system

This thesis investigates the process of mitochondrial biogenesis in the rodent CNS in the context of neuroinflammatory and neurodegenerative disease. There is mounting evidence of mitochondrial damage in neuroinflammation but very little is known about the turnover of mitochondria in neurones. We developed a method to assess mitochondrial biogenesis by tagging replicating mitochondrial DNA with bromodeoxyurine (BrdU), and used the method to examine mitochondrial biogenesis. In healthy motor neurons, mitochondria were distributed throughout the cell, including the axons, but the DNA replication signal initially only appeared in the cell body, subsequently becoming distributed away from the soma suggesting the presence of a mitochondrial ‘nursery’ in the cell body of long neurones. Furthermore, neuronal DNA replication increased in response to raised energy demand resulting from unilateral electrical stimulation of the sciatic nerve, indicating that mitochondrial biogenesis is promptly responsive to energy demand. Mitochondrial biogenesis was also examined in spinal cord neurons in a model of multiple sclerosis (experimental autoimmune encephalomyelitis; EAE), and the degree of mtDNA replication was compared with the amount of inflammation in the tissue. We found that in severely inflamed tissue mitochondrial biogenesis was significantly reduced in the motor neurones. However, under subtle inflammation in EAE as well as with local intraspinal injection of LPS (lipopolysaccharide), there was an increase in mitochondrial biogenesis, which may be a compensatory mechanism. In separate experiments the CNS was examined globally using the BrdU method, which revealed the presence of hotspots of neuronal mtDNA replication indicating marked differences in mitochondrial turnover. Interestingly, these hotspots represented regions known to undergo degeneration in neurological diseases, especially those known or suspected to have a mitochondrial component in their aetiology. The current findings reveal that mitochondrial biogenesis is substantial in neurons with long axons, and that it is promptly responsive to changing energy and disease conditions.
Aphid activities during sieve element punctures

Aphid salivation in sieve elements and phloem sap ingestion were linked to waveforms in the Electrical Penetration Graph (EPG). Non‐viruliferous Rhopalosiphum padi (L.) (Hemiptera, Aphididae) on barley yellow dwarf virus (BYDV) infected wheat could acquire the virus, which was used as an indication for phloem sap ingestion, whereas virus inoculation by viruliferous aphids on healthy plants was associated with salivation in sieve elements or other phloem cells. Probing was monitored and the waveforms recorded were related to ELISA results of test plants. The EPG patterns A, B, and C are indicative of the stylet pathway phase, whereas patterns E1 and E2 reflect the phloem (sieve element) phase with an unknown activity (E1) or with ingestion and concurrent salivation (E2). Aphids showing pathway and E1 rarely acquired virus, suggesting that little or no phloem sap ingestion can occur during these patterns, whereas those showing additionally pattern E2 did so substantially, indicating phloem sap ingestion. The main pattern related to virus inoculation was E1, although some aphids were able to inoculate plants during pathway. Pattern El clearly reflects the most important salivation into sieve elements. Pattern E2 had no clear contribution to virus inoculation, supporting the present hypothesis that during this pattern the saliva is mixed with the phloem sap in the single canal at the stylet tips and ingested immediately, without reaching the plant tissue. Sustained sap ingestion did not affect virus inoculation. So, BYDV inoculation mainly occurs during the first period of a sieve element puncture which is always formed by E1. Implications on persistent virus transmission are discussed.
Binding of Paxillin to the α9 Integrin Cytoplasmic Domain Inhibits Cell Spreading*

α9β1 integrin is a member of the β1 integrin family, plays an important role in extravasation of neutrophils at sites of acute inflammation, and is required for the normal development of the lymphatic system. The α9 and α4 integrin subunits are most closely related and form a subfamily of integrin α subunits. Previously, we have reported that the α4 cytoplasmic domain directly and tightly binds paxillin, an intracellular signaling adaptor molecule. This interaction accounts for some of the unusual functional responses to α4 integrin-mediated cell adhesion, including stimulation of cell migration and inhibition of cell spreading and focal adhesion formation. In the current studies, we have examined the interaction between the α9 cytoplasmic domain and paxillin. Here we report that the α9cytoplasmic domain binds paxillin directly and tightly and that the α9-paxillin association inhibits cell spreading. We have identified amino acid residues in the α9 cytoplasmic domain, Trp999 and Trp1001, that are critical for paxillin binding, and alanine substitution of either Trp999 or Trp1001 blocks paxillin binding. Furthermore, these mutations also reverse the effect of the α9 cytoplasmic domain on cell spreading. Thus, the α9 and α4 integrin subunits form a paxillin-binding subfamily of integrin α subunits, and direct binding of paxillin to the α9 cytoplasmic domain mediates some of the biological activities of the α9β1integrin.
The Breeding Behavior and Tumor Incidence of a Black Agouti Stock of Mice

This is the third in a series of communications to be published on the breeding behavior and tumor incidence of the inbred strains of mice used for experimental purposes in our laboratory. Data on the dilute brown strain were published by Murray in 1934. Comparative tabulations on the albino or A stock have also been made (Bittner). Both strains have a high incidence of mammary gland tumors. In addition, primary lung tumors were comparatively common in representatives of the A stock, being observed in mice of both sexes. In this article we shall describe the C3H or Z stock, which, like the dilute brown and albino strains, has a high mammary tumor incidence. Mention was made of this strain in a previous report, (3). Origin of the Stock: The stock was started in 1918 by Dr. L. C. Strong, who crossed individuals of the dilute brown and albino strains. The albino mice at that date carried the black agouti factor, and only animals having the coat color of wild mice were selected as breeders. This race has been continued by mating brothers to sisters. It had been inbred for twenty-one generations when representatives were obtained from Strong; twelve additional generations have been raised. Care has been taken to select only the sublines in which no breeding females died non-cancerous. One line is being bred which has in its direct ancestry twenty successive generations of mammary tumors.
Linking Endosomal Traffic and PAMP-triggered Immunity in Plants

One of the first layers of active defense in plant-microbe interactions is based upon the recognition of pathogen associated molecular patterns (PAMPs). Although biochemically well studied, components of PAMP signaling await to be identified. Furthermore, emerging data point to a function of endocytosis in signaling (Chinchilla et al., 2007a; Geldner et al., 2007). Here, we conducted reverse and forward genetic approaches to identify components and to elucidate the role of endocytosis in PAMP signaling. Previous successful forward genetic approaches were refined to identify additional components in PAMP signaling (Gomez-Gomez and Boller, 2000). The sensitivity of the response to flg22 by seedling growth inhibition was enhanced by UV-B treatment (Logemann and Hahlbrock, 2002), and by employing a modified seedling growth inhibition assay on plates with reduced flagellin dosis. Arabidopsis thaliana ecotypes were inspected and most insensitive accessions were mutated in FLS2 alleles. Furthermore, screening a a-irradiation population revealed several fli mutants (for flagellin-insensitive). Notably, only late PAMP responses such as callose deposition, seedling growth arrest and resistance to PtoDC3000 infection were impaired. The tested fli1-8 mutants were not allelic to FLS2 or BAK1, which suggests that yet unknown components of flg22 signaling are affected. While fli mutants were more susceptible to bacterial infection they appear more resistant to the oomycete Hyaloperonospora arabidopsis cv. Cala2. Taken together, potentially novel components involved in late PAMP responses were identified. FLS2 endocytosis is one of the flg22 responses and appears to contribute to flg22 signaling. We therefore tested several knock-out mutants in known endocytosis components for their response to flg22 and bacterial infection. While most mutants displayed wild-type-like flg22 responses, vps28-2, vps37-1, vps28-1 elch, and gnl1-1 exhibited enhanced susceptibility to PtoDC3000 infection. VPS28-2, VPS37-1, and VPS28-1 ELCH are components of the ESCRT I system responsible for sorting ubiquitinated proteins. GNL1 is an ARF GEF regulating vesicle trafficking at the Golgi and PM. To further delineate the role of endocytosis in plant immunity, a genetic screen for novel endocytosis mutants was established. Applying quantitative confocal microscopy 12 fel mutants (for FYVE-GFP endosome levels) with altered endosomal numbers in cotyledons were identified. Two selected mutants, fel4 with an increased endosome number and a few enlarged endosomes and fel5 with a reduced endosome number, were characterized in more detail. Both fel mutants displayed minor developmental defects, which did not co-segregate with the endosomal phenotype, and revealed unaltered endosomal levels in roots. In total, these approaches allowed us to isolate novel components involved in PTI and components regulating endocytosis in Arabidopsis. Map-based cloning will unravel the genetic identity of these mutants and elucidate how endocytosis contributes to immunity.
A review of cellulosic biofuel commercial‐scale projects in the United States

In contrast to a few years ago, when cellulosic ethanol via enzymatic hydrolysis was the only widely recognized technology for commercially producing cellulosic biofuels, a diversity of approaches are currently under commercial development. While no commercial‐scale (≥20 million gallons per year) cellulosic biofuel facilities are operating at present, at least ten biorefinery projects employing six different pathways are expected to begin operations by 2014. These biorefineries will employ the following pathways: (i) catalytic pyrolysis and hydrotreating to hydrocarbons; (ii) gasification and Fischer‐Tropsch synthesis to hydrocarbons; (iii) gasification and methanol‐to‐gasoline synthesis; (iv) dilute acid hydrolysis, fermentation to acetic acid, and chemical synthesis to ethanol; (v) enzymatic hydrolysis to ethanol; and (vi) consolidated bioprocessing (single‐step enzyme production, hydrolysis, and fermentation) to ethanol. This review provides an overview of the six pathway technologies, comprehensive descriptions of each of the ten biorefinery projects, and a discussion of the current direction of cellulosic biofuel commercialization efforts and its implications for the revised Renewable Fuel Standard. © 2013 Society of Chemical Industry and John Wiley & Sons Ltd
Trapping and handling squirrels: Trap modification and handling restraint to minimize injuries and stress

Trapping and handling is stressful for wild animals and may result in injuries. Minimizing stress and injuries is important not only for the welfare of the animals, but to assure integrity of research using trapped wild animals. By recording injury rates associated with trapping and handling, it is possible to assess the welfare performance of trapping and handling methods. Although the International Organization for Standardization published a standardized scale for the type and severity of injuries caused by trapping and handling (ISO 1999), it does not provide guidelines for acceptable standards of animal welfare; that is left to the researchers themselves to determine. The purpose of this paper is to measure the level of injury to wild squirrels caused by trapping and handling using minimally disruptive methods. We report our injury rates from several studies conducted in California, USA, that used various trapping and handling methods and the refined procedures we have adopted. Our data set on multiple Sciuridae species provides values for comparison with other studies. We found that using a canvas cover for traps minimized stress and injuries in captured squirrels. We also found that using a cone handling bag minimized handling time and stress associated with handling and eliminated the need for chemical immobilants. Further, we found that covering the animals' eyes during handling appeared to reduce visible signs of stress. © 2013 The Wildlife Society.
The lizard genus Phenacosaurus

Examination of 64 specimens of this endemic Colombian genus in the collections of the Instituto de Ciencias Naturales, the Instituto de La Salle in Bogota, and the Colegio San Jose in Medellin indicates that the genus is not monotypic but is composed of at least three species. The genus Phenacosaurus was described by Barbour in 1920 (Proc. New England Zool Club, 7, pp. 61-63) with Anolis heterodermus Dumeril as the monotype. The genus is close to Anolis, being distinguished by having a prehensile tail, a dorsal crest of enlarged scales, heterogeneous dorsal scalation of larger and smaller scales intermixed, and by having more or less of a casque, the hind end of the head being elevated and projecting backward somewhat over the body. Anolis jacare, of Norte de Santander and adjacent Venezuela, may be close to the parent stock of Phenacosaurus.
How many Archaeolacerta inhabit the Corso-Sardinian Plate? Allozyme variation and differentiation in Archaeolacerta bedriagae (Camerano, 1885)

Archaeolacerta bedriagae is a rock lizard endemic to Corsica and Sardinia. Four subspecies have been recozied to date on the basis of morphological traits. Previous allozyme investigations revealed high genetic differentiation among populations of the species. Based on these results some authors hypothesized that more than one species of Archaeolacerta may occur on Corsica and Sardinia. In this paper we investigated allozyme variation at 19 gene loci in 5 populations belonging to all subspecies of A. bedriagae in order to study genetic differentiation among populations from Corsica and Sardinia, and to compare our results with those obtained in previous studies carried out on allozyme variation and taxonomy of the species. Low levels of genetic differentiation (average Nei's D = 0.026) and heterogeneity (mean FST = 0.147) were found comparing the A. bedriagae populations, and there was no evidence of interruption or restriction of gene flow. This is in agreement with the available molecular and morphometric data, while it is not in accordance with allozyme data reported in the previous studies. Our data do not support the hypothesis of an unrecognized criptic species of Archaeolacerta in Corsica and Sardinia, and indicate that the definitive assessment of the taxonomic status of the A. bedriagae populations requires further investigation.
Long-term trends in catch and effort of commercial linefish off South Africa's Cape Province: snapshots of the 20th century

The Cape commercial linefishery, established during the first half of the 19th century, currently consists of about 2 500 vessels (±20 000 crew), which land some 15 500 tons of fish each year. In spite of a long history, a lack of a long-term catch and effort data series has severely hindered the management of the fishery. This paper providcs commercial catch and effort data for three periods during the 20th century: 1897–1906, 1927–1931 and 1986–1998. Trends in catch per unit effort (cpue) were verified with additional data from the inshore trawl-fishery, from fishery-independent surveys and, where possible, stock assessment. According to a Linefish Management Protocol developed for the Linefishery, any stock demonstrating a historical reduction in cpue or catch contribution of more than 75% is to be regarded as overexploited. Evaluations based on present datasets support this arbitrarily determined reference point for cpue, but reveal that catch composition is a poor indicator of stock status and should be used with caution. In spite of technological advances such as the advent of combustion engines, nylon lines. echo-sounders, electronic navigational aids, onboard freezer facilities and larger vessels, declines in catch rate indicative of severe overexploitation (i.e. 75–99%) were observed for many important linefish species during the 20th century. Most of these were higher-trophic-Level species from the warm/temperate East Coast, several of which are also endemic. Life-history characteristics of the vulnerable species (i.e those demonstrating declines in cpue of >75%) include predictable location in time and space (either coastal migrant or resident), longevity (>15 years) and late maturity (relative to maximum age). Apart frorreduced productivity associated with stock depletion, other setbacks, such as ecosystem alteration, loss of genetic diversity and shor-term commercial extinction, are also anticipated. In order to rebuild depleted linefish stocks it is deemed essential to create additional marine reserves, dramatically improve enforcement, develop extensive public awareness programmes and substantially reduce commercial effort.
Immunocytochemical detection and location of the membrane-bound nitrite oxidoreductase in cells of Nitrobacter and Nitrospira

The intracellular location of the membrane-bound nitrite oxidoreductase of Nitrobacter hamburgensis X14 was determined by electron microscopic immunocytochemistry. Post-embedding labeling performed on ultrathin sections revealed that the enzyme was located at the cytoplasmic membrane and at the intracytoplasmic membranes. As shown by immunonegative staining of isolated membranes the labeling of the monoclonal antibodies named Hyb 153-2 and Hyb 153-3 was located at the cytoplasmic side of the membranes. Using Hyb 153-2, which recognize the α-subunit of nitrite oxidoreductase, the labeling was found at the surface of the paniculate membranes. In contrast, Hyb 153-3, recognizing the β-subunit of nitrite oxidoreductase, bound preferably at the periphery of the membrane fragments. Besides Nitrobacter, Hyb 153-3 also recognized the nitrite-oxidizing system in two strains of Nitrospira. No reaction was found with Nitrospina and Nitrococcus.