Miracle-dz/UniFAR-FTUs huggingface dataset:
Biocontrol of Morganella morganii subsp. morganii and Histamine Accumulation in Tuna Meat by Treatment with a Lytic Bacteriophage

Histamine poisoning is a common seafood-borne illness worldwide, and Morganella morganii subsp. morganii is one of the most probable histamine producers. Bacteriophages are bacterial viruses that kill the host cell after infection. In this study, we evaluated the effect of M. morganii phage FSP1 treatment on histamine accumulation by M. morganii in raw tuna meat. M. morganii was inoculated to tuna meat and incubated at 4, 12 and 20°C to evaluate the inhibitory effects of FSP1 on the growth and histamine accumulation of M. morganii. Viable M. morganii counts were decreased significantly in response to FSP1 treatment under all conditions. Furthermore, histamine concentrations in phage-treated samples were significantly lower than those of control samples. FSP1-resistant M. morganii did not develop after FSP1 treatment. These results suggest that phage treatment might be an effective tool to reduce the risks of histamine poisoning by M. morganii in fisheries products.
Retribución de la alta dirección, estructura del consejo de administración y resultados

espanolResultados empiricos previos muestran distintas contradicciones cuando se relaciona la retribucion de los miembros del equipo de alta direccion, la estructura del consejo de administracion y los resultados alcanzados por la empresa. Un menor numero de consejeros y una mayor proporcion de consejeros externos se asocian a una mayor supervision, pero no hay consenso sobre el efecto en el nivel retributivo del equipo de alta direccion. Esta falta de consenso se agrava cuando se analiza el efecto sobre los resultados. En este trabajo ofrecemos un marco teorico y un estudio empirico basado en la metodologia de datos de panel, que permite explicar por que los analisis previos difieren. En el contexto del mercado espanol se confirman las perspectivas del procesamiento de la informacion, que vinculan la sobredimension del consejo con una mayor retribucion del equipo de alta direccion. Asimismo, la mayor proporcion de consejeros externos reduce el nivel retributivo del equipo de alta direccion al aumentar la supervision y reducir el poder de los internos. Por ultimo, se obtiene una relacion cuadratica entre los resultados de la empresa y la retribucion del equipo de alta direccion. Esta relacion permite explicar, conjuntamente, un efecto positivo, defendido desde la teoria de la agencia, sobre los resultados de la empresa a niveles bajos de retribucion de los miembros del equipo alta direccion y un efecto negativo, como consecuencia de una mayor discrecion de estos a niveles altos. EnglishPrevious empirical results reveal various contradictions when relating top management compensation, board structure and levels of performance. While fewer directors and more external directors is associated with better supervision, there is no agreement on the effect on top management compensation level. This lack of consensus is even more noticeable when analysing the effect performance. This paper offers a theoretical framework and a panel data methodology based empirical study to account for how earlier analyses have differed. Given the great board dimension in the Spanish market, information processing perspectives are confirmed which link positively board size with higher top management compensation. Similarly, a higher proportion of external directors reduces top management compensation level since it improves supervision and reduces insiders� power. Finally, a quadratic relation is obtained between performance and top management compensation. This relation explains both a positive effect, supported by agency theory on performance at low levels of management compensation, and a negative effect as a consequence of higher managers� discretion at high levels.
IJSRD || National Conference on Inspired Learning || October 2015

Alzheimer’s disease (AD) is characterized by a widespread functional disturbance of the human brain. It may be caused by the deposition of amyloid beta-peptide (Aβ) in plaques in brain tissue. In AD, there is the formation of neurofibrillary tangles containing tau protein, which is proposed to result from an imbalance between the production and clearance of amyloid beta-peptide (Aβ). The degradation and production of Aβ is significantly regulated by low-density lipoprotein receptor-related protein, LRP1, which is a large endocytic receptor. The LRP1 is known to regulate this function by interacting with a novel and specific interactor, NYGGF4 (phosphotyrosine interaction domain containing 1). NYGGF4 is known to be differentially expressed during AD progression. Here, we are trying to computational predict the interaction of LRP1 and NYGGF4 through protein structure prediction and protein-protein interaction.
The differential apoptotic effects of Vpr and Vpx of human and simian immunodeficiency viruses in mammalian cells

Previously published results from our laboratory have shown that HIV1 Vpr has both cytostatic and cytotoxic effects in the fission yeast Schizosaccharomvces pombe. We transiently transfected different vpr and/or vpx genes from different primate Ientiviruses into a variety of marnmalian ce11 fines from different species. These results showed that : 1) HIV-1 Vpr induces apoptosis in human ceils (HeLa, TE671 and 293) but not in chimpanzee cells (fl LSK), Afican green monkey cells (Vero) and rodent cells (CHTG49, A9 and P388D1). 2) In contrast, Vpr andlor Vpx of HIVZ, SIVrnac239 and Vpx of SNagm do not induce apoptosis in any of the ce11 lines rnentioned above. 3) When the HN-1 vpr gene was cotransfected with a reporter gene, GFP, about 90% of the apoptotic cells were GFP-positive, suggesting that HIV-I Vpr does not induce apoptosis through paracrine or bystander route. 4) The apoptotic effect of HIV-1 Vpr can be regulated by cotransfecting with different members of Bcl-2 gene family, suggesting that the Bcl-2 family members may be involved in the mechanism of HIV-I Vpr-induced apoptosis.
Naturally occurring variation in the promoter of the chromoplast-specific Cyc-B gene in tomato can be used to modulate levels of ß-carotene in ripe tomato fruit

ii Acknowledgments. iv Vita . v List of Tables . viii List of Figures . ix Chapter 1: Introduction . 1 Carotenoids . 1 β-carotene . 2 Carotenoid biosynthesis in tomato . 4 Classical characterization of the B locus . 7 Molecular characterization of the B locus . 8 Exploring allelic variation through sequencing . 8 Backcrossing . 10 Marker-assisted backcrossing . 10 Rationale and Significance . 14 Approach . 16 Project Aim . 20 Chapter 2: Sequencing the promoter of the chromoplast-specific Cyc-B gene in tomato reveals novel high β-carotene alleles and putative functional mutations . 21 Acknowledgments.21 Abstract . 22 Introduction . 23 Materials and Methods . 25 vii Results . 31 Discussion . 35 Chapter 3: Naturally occurring variation in the promoter of the chromoplast-specific CycB gene in tomato can be used to modulate levels of β-carotene in ripe tomato fruit . 46 Acknowledgments.46 Abstract . 47 Introduction . 48 Materials and Methods . 52 Results . 58 Discussion . 61 Chapter 4: Conclusion.72 References . 76 Appendix A: SNPs used for background genome selection in BC1 . 85 Appendix B: SNPs used for background genome selection in BC2.88
Optimization of selection for two identified quantitative trait loci.

Selection to improve a single trait, where polygenic effects and two quantitative trait loci (QTL) both affected phenotype, was optimized by using a genetic algorithm for different values of additive effects, dominance effects and epistasis effects for the two QTL. The method accounted for gametic phase disequilibrium among polygenes and between QTL and polygenes. The extra cumulative discounted response (CDR) from optimal selection over genotypic selection depended on magnitude of additive and dominance effects of QTL. Maximum extra CDR from optimal selection with two QTL was 2.2% for additive QTL and 6.7% for dominant QTL while corresponding values from optimal selection with a single QTL were 2.1% and 5.3%. Benefit from optimal selection was decreased by additive-by-additive epistasis and increased by additive-by-dominance epistasis or dominance-by-dominance epistasis. It is most useful to optimize selection when QTL effects are dominant and when additive effects are between 0.25 and 2.0 times the genetic standard deviation.
Comparative evaluation of harada–Mori and agar plate culture for the identification of hookworm species under limited resources

Background: Human hookworm infection has widespread socioeconomic and public health implications. Several coproculture techniques have been developed for morphological identification of hookworm larvae under limited resource availability. The objective of this study was to compare the performances of Harada–Mori culture (HMC), agar plate culture (APC), and modified APC (MAPC) of hookworm positive stool specimen for identification of hookworm species occurring in East Sikkim, India. Materials and Methods: This prospective cohort study was performed using 180 stool specimen collected from children who attended Central Referral Hospital and Sir Thodup Namgyal Memorial Hospital, with the complained of gastrointestinal symptoms. Blood samples were also collected to correlate with the complete blood count (CBC). The hookworm positive stool specimen evaluated by microscopy was subjected to HMC, APC, and MAPC techniques to harvest hookworm larvae. Stoll's dilution egg count for determining egg intensity and CBC were also performed for the children who were positive for hookworm's eggs in their stool sample. Results: This study observed a predominance of Necator americanus (75%) over Ancylostoma duodenale (25%). CBC results showed high packed cell volume values in 9/12, low hemoglobin 9/12, and high eosinophil count in all the positive children. Stoll's dilution egg count showed moderate infection in 66.6%, light and heavy infections in 16.7% of children's. APC method was superior to HMC and MAPC in culturing and identifying hookworm species. Conclusions: APC was observed to yield better results and was easier to perform in limited resource laboratory setting compare to MAPC or Harada–Mori culture techniques.
Effects of hatching time and hatching system on broiler chick development

Key words: hatching time, hatching system, chick physiology, broiler growth, chick quality. Chicks hatch over a time window of 24-36 hours and are only removed from the hatcher when the majority of the chicks have hatched. Especially for the early hatching chicks this leads to delays in the first feed and water access and consequently negative effects on chick development. In an alternative hatching system, named Patio, the hatching and brooding phase are combined, thereby enabling direct posthatch feed and water access. Environmental conditions in Patio differ from those in hatchers, which may further influence chick quality, physiology, and growth. Chicks hatching at different moments may respond differently to these different conditions in both hatching systems. In this thesis, the first aim was to determine effects of hatching in the Patio system on hatchability, chick quality, and growth. The second aim was to determine the physiological status of chicks of different hatching moments, in the hatcher and the Patio system, at hatch, and at chick collection (21.5 d of incubation). Effects of hatching time and moment of first feed and water access on posthatch growth were also included. Hatchability of fertile eggs was 1.03% higher in the Patio system compared to the hatcher, which was probably due to different climate conditions during the hatching phase. At hatching, chick physiology was not clearly affected by hatching system, but effects of moment of hatching in the hatch window were clear: longer incubation times led to increased organ weights and decreased yolk weights, suggesting a higher level of maturation in late hatching chicks. At the moment of chick collection, Patio chicks, having immediate feed and water access,showed larger body and organ weights, higher hepatic glycogen reserves, higher plasma glucose and T3 levels, and lower corticosterone levels compared to hatcher chicks which were fasted between hatching and chick collection. Usinga chick qualitative score based on physical traits and the incidence of second grade chicks, chick quality was lower in Patio than in hatcher chicks. However the quality scores used were not predictive for posthatch performance. Patio chicks showed improved posthatch growth compared to hatcher chicks, which was not related to different climate conditions during hatching, but to earlier feed and water access. Apart from higher growth from d0-7 in early and midterm vs late hatching chicks, effects of hatching time on growth were not clear from this thesis. In conclusion, despite considerable differences in climate and other environmental factors, effects of hatching system on physiology of broiler chickens at hatch and growth performance up to slaughter age are limited. Perinatal chick physiology is affected by the moment of hatching in the hatch window, and by posthatch conditions in the hatching system, especially early feed and water access.
PorSignDB: a database of in vivo perturbation signatures for dissecting clinical outcome of PCV2 infection

Porcine Circovirus Type 2 (PCV2) is a pathogen that has the ability to cause often devastating disease manifestations in pig populations with major economic implications. How PCV2 establishes subclinical persistence and why certain individuals progress to lethal lymphoid depletion remain to be elucidated. Here we present PorSignDB, a gene signature database describing in vivo porcine tissue physiology that we generated from a large compendium of in vivo transcriptional profiles and that we subsequently leveraged for deciphering the distinct physiological states underlying PCV2-affected lymph nodes. This systems biology approach indicated that subclinical PCV2 infections shut down the immune system. A robust signature of PCV2 disease emphasized that immune activation is dysfunctional in subclinical infections, however, in contrast it is promoted in PCV2 patients with clinical manifestations. Functional genomics further uncovered IL-2 as a driver of PCV2-mediated disease and we identified STAT3 as a druggable PCV2 host factor candidate. Our systematic dissection of the mechanistic basis of PCV2 reveals that subclinical and clinical PCV2 display two diametrically opposed immunotranscriptomic recalibrations that represent distinct physiological states in vivo, which suggests a paradigm shift in this field. Finally, our PorSignDB signature database is publicly available as a community resource (http://www.vetvirology.ugent.be/PorSignDB/, included in Gene Sets from Community Contributors http://software.broadinstitute.org/gsea/msigdb/contributed_genesets.jsp) and provides systems biologists with a valuable tool for catalyzing studies of human and veterinary disease. Author Summary Porcine Circovirus Type 2 (PCV2) is a small but economically important pathogen circulating endemically in pig populations. Although PCV2 causes mostly chronic subclinical infections, many individuals develop a lethal form of circoviral disease consisting of a collapse of lymphoid tissue. In order to provide a fresh look at how PCV2 reprograms host tissue, we created PorSignDB, a compendium of hundreds of transcriptomic gene-expression signatures derived from primary porcine tissue specimens of well over 1500 patients or lab animals. By leveraging PorSignDB on transcriptomic data of PCV2 patients, we uncover that subclinical PCV2 reprograms the host into a striking state of non-infection, which explains its failure to respond to an initial phase of circoviral presence. A PCV2 disease signature further demonstrates that the silenced immune system associated with subclinical PCV2 becomes fully activate in PCV2 patients, triggering severe circoviral disease. Further genomic and functional analysis demonstrate STAT3 as a druggable host factor and IL-2 as a disease driver. Together, this study demonstrates the mechanistic underpinnings of clinical outcome of PCV2 infections: subclinical and clinical PCV2 display two entirely opposing transcriptomic recalibrations of lymphoid tissue.
Genome report: A duplication lost in sugarcane hybrids revealed by chloroplast genome assembly of wild species Saccharum officinarum

Sugarcane is a crop of paramount importance for sustainable energy. Modern sugarcane cultivars are derived from interspecific crosses between the two wild species Saccharum officinarum and Saccharum spontaneum and this event occurred very early in the sugarcane domestication history. This hybridization allowed the generation of cultivars with complex aneuploidy genomes containing 100–130 chromosomes that are unequally inherited - ~80% from S. officinarum, ~10% from S. spontaneum and ~10% from inter-specific crosses. Several studies have highlighted the importance of chloroplast genomes (cpDNA) to investigate hybridization events in plant lineages. Few sugarcane cpDNAs have been assembled and published, including those from sugarcane hybrids. However, cpDNAs of wild Saccharum species remains unexplored. In the present study, we used whole-genome sequencing data to survey the chloroplast genome of the wild sugarcane species S. officinarum. Illumina sequencing technology was used for assembly 142,234 bp of S.officinarum cpDNA with 2,065,893 reads and 1043x of coverage. The analysis of the S. officinarum cpDNA revealed a notable difference in the LSC region of wild and cultivated sugarcanes. Chloroplasts of sugarcane cultivars showed a loss of a duplicated fragment with 1,031 bp in the beginning of the LSC region, which decreased the chloroplast gene content in hybrids. Based on these results, we propose the comparative analysis of organelle genomes as a very important tool for deciphering and understanding hybrid Saccharum lineages.
Co-Expression of a Suicide Gene in CAR-Redirected T Cells Enables the Safe Targeting of CD44v6 for Leukemia and Myeloma Eradication

Abstract 949 Background: Acute myeloid leukemia (AML) and multiple myeloma (MM) share common features, such as preferential homing to the bone marrow (BM) and the tendency to relapse after chemotherapy. These phenomena are possibly linked, as signals provided within the BM niche induce chemoresistance. Relapsing AML and MM can however be cured by allogeneic hematopoietic stem cell transplantation (HSCT), suggesting that allospecific T may specifically sterilize tumor cells that survive chemotherapy. Unfortunaley, the universal application of HSCT is severely limited by the occurrence of life-threatening GVHD and by the fact that leukemia often escapes the alloimmune pressure by losing specific HLAs, as we have recently demonstrated (Vago et al., NEJM 2009). The isoform variant 6 of the adhesion receptor CD44 (CD44v6) is widely expressed in AML and MM, and is crucially involved in BM homing. In phase I/II trials, targeting CD44v6 with mAb conjugated to chemotherapeutic agents showed substantial efficacy, but also toxicity due to background expression of CD44v6 on the skin. Thanks to the chimeric antigen receptor (CAR) technology it is now possible to efficiently redirect T cells against virtually any antigen for which there is availability of a specific mAb. Our experience with suicide gene therapy in the context of HSCT (Ciceri et al., Lancet Oncol 2009) clearly indicates that genetic switches are efficient tools for controlling the off-tumor toxicities of T cells. Aim: To develop a strategy for the safe targeting of CD44v6 through the co-expression of a suicide gene in CAR-modified T cells for AML and MM treatment Results: CD44v6 surface expression was observed in 11/14 (79%) AML cases. Co-culturing primary leukemic cells with BM-derived mesenchymal stromal cells (MSCs) ex vivo caused the significant up-regulation of CD44v6 expression (P Conclusions: CD44v6 CAR-redirected suicidal T cells have the potential to eradicate AML and MM and can be ablated at will. We are currently designing a phase I/II clinical trial where CD44v6 CAR-redirected suicidal T cells will be applied soon after autologous HSCT for sterilizing residual tumor, and routinely ablated thereafter not to interfere will full hematological reconstitution. The co-expression of a suicide gene will also allow to control any potential toxicity deriving from background expression of CD44v6 on healthy tissues. Disclosures: Bordignon:Molmed SpA: Employment.
Behavioral plasticity in a variable environment: snow depth and habitat interactions drive deer movement in winter

In seasonally varying environments, animals should alter habitat selection through time to avoid the harshest conditions. Winter severity is limiting for many ungulates in high-latitude ecosystems, and quality of habitat is an important determinant of winter survival. Previous studies in Southeast Alaska indicated that Sitka black-tailed deer (Odocoileus hemionus sitkensis) selected old-growth forest that provides both snow interception and forage, but with great variability among studies, years, and geographic areas. Clearcut timber harvest has greatly reduced the extent and quality of old-growth forest. The value of 2nd-growth and old-growth forest types to deer likely depends on snow depth, which is highly variable in space and time. We measured selection for vegetation classes, landscape features, and forage biomass by monitoring 56 GPS-radiocollared adult female deer from 1 January to 1 April between 2011 and 2013. Simultaneously, we measured snow depth across deer home ranges daily. We determined that snow depth had a strong effect on selection for vegetation classes. During periods of low snow, deer selected young 2nd growth but avoided old 2nd growth and high-volume old growth. As snow depths increased, young 2nd growth was avoided and deer selected old 2nd-growth and productive old-growth forests. The composition of vegetation classes within the landscape influenced selection, with deer selecting locally abundant habitats. These behaviors suggest that the widespread distribution of forest patches that provide snow interception and forage biomass may be critical to fulfilling the energetic requirements of deer during winters with snow. Such context-dependent habitat selection is likely widespread among wildlife species in variable environments and should be incorporated into study design and analysis.
Isolation and Identification of Serratia marcescens from Bovine Mastitis infections in Iraq and their Susceptibility to Antibiotics

This study was conducted to isolate Serratia marcescens from bovine mastitis for the first time in veterinary medicine field in Iraq and their susceptibility against antibiotics. One hundred and fifty samples from case of mastitic milk of cow were collected from College of University of Baghdad/College of Veterinary Medicine, University of Baghdad/College of Agriculture, Dora zone, Radhwanya zone and Abu-Ghraib zone. Cultured by selective and differential media then Gram stain were done. After purification of cultured bacteria biochemical tests were done and confirmed by API 20 E System and RapID ONE System kit. Results showed that 6 (4%) samples out of 150 samples were positive for Serratia marcescens and it’s the first time to isolate in veterinary medicine field. The resistance of these isolates against antibiotics Gentamycin (30 mg), Imipenem (10 mg),Ciprofloxacin (5 mg),Nalidixic acid (30 mg), Ampicillin (10 mg), Cefotaxime (30 mcg), Amikacin (30 mg), Chloramphenicol (30 mg), Tetracyclin (10 mg) and Amoxicillin-Clavulanic acid (20/10 mg) were studied. The results showed that Serratia marcescens were resistant 100% to Ampicillin, Imipenem and Tetracyclin, 66.66% to Cefotaxime and susceptible 100% to Ciprofloxacin, 83.33% to Gentamycin, 66.66% to Chloramphenicol and 50% to Nalidixic acid. While Intermediate 83.33% to AmoxicillinClavulanic acid, 50% to Nalidixic acid and 33.33% to Chloramphenicol and Cefotaxime.