Miracle-dz/UniFAR-FTUs huggingface dataset:
Corticocortical signaling drives activity in a downstream area rapidly and scalably

How effectively does activity in an upstream cortical area drive activity in a downstream area? To address this, we combined optogenetic photostimulation with multi-unit electrophysiology to study a parietofrontal corticocortical pathway from retrosplenial cortex to posterior secondary motor cortex in mice. Photostimulation in the upstream area produced local activity that decayed quickly. This activity in turn drove downstream activity that arrived rapidly (5-10 ms latencies), and scaled in amplitude across a wide range of stimulus parameters as an approximately constant fraction (~0.2) of the upstream activity. A model-based analysis could explain the corticocortically driven activity with exponentially decaying kernels (~20 ms time constant) and small delay. Reverse (antidromic) driving was similarly robust. The results show that corticocortical signaling in this pathway drives downstream activity in a mostly linear manner. The regular and predictable responses further suggest that precise stimulation driven control of cortical population activity should be possible.
Fire history in southern Patagonia: human and climate influences on fire activity in Nothofagus pumilio forests

Fil: Mundo, Ignacio Alberto. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Laboratorio de Dendrocronologia e Historia Ambiental; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina
The Identification and Targeting of Partially-Folded Conformations on the Folding Free-Energy Landscapes of ALS-Linked Proteins for Therapeutic Intervention: A Dissertation

The hallmark feature of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), is the accumulation of cytoplasmic inclusions of key diseaselinked proteins. Two of these proteins, TDP-43 and SOD1, represent a significant proportion of sporadic and familial ALS cases, respectively. The population of potentially aggregation-prone partially-folded states on the folding free-energy landscape may serve as a common mechanism for ALS pathogenesis. A detailed biophysical understanding of the folding and misfolding energy landscapes of TDP-43 and SOD1 can provide critical insights into the design of novel therapeutics to delay onset and progression in ALS. Equilibrium unfolding studies on the RNA recognition motif (RRM) domains of TDP-43 revealed the population of a stable RRM intermediate in RRM2, with residual structure localized to the N-terminal half of the domain. Other RRM domains from FUS/TLS and hnRNP A1 similarly populate RRM intermediates, suggesting a possible connection with disease. Mutations, which enhance the population of the RRM2 intermediate, could serve as tools for deciphering the functional and misfolding roles of this partially-folded state in disease models, leading to the development of new biomarkers to track ALS progression. ALS mutations in SOD1 have been shown to destabilize the stable homodimer to result in increased populations of the monomeric and unfolded forms of SOD1. Mechanistic insights into the misfolding of SOD1 demonstrated that the unfolded state is a key species in the initiation and propagation of aggregation, suggesting that limiting
CCDC6 (coiled-coil domain containing 6)

CCDC6 gene product is a pro-apoptotic protein substrate of ATM whose loss or inactivation enhances tumor progression. In primary tumors the impaired function of CCDC6 protein has been ascribed to CCDC6 rearrangements, to somatic mutations and to CCDC6 different levels in several neoplasia. The CCDC6 turnover is regulated in a cell cycle dependent manner upon post-translational modification events. The impairment of CCDC6 turnover may affect cells behaviour and drug response.
Feature Article : Growth Factors and Signaling Pathways in the ChondrogenicDifferentiation of Mesenchymal Stem Cells

Mesenchymal stem cells (MSCs) are multipotent progenitor cells that can differentiate into the severallineages. MSC has drawn an enormous attention because of the potential for use in tissue engineering and regener-ative medicine. Several growth factors and signaling mechanisms strongly influence chondrogenic differentiation of MSCs. In this review, we summarized the roles of these growth factors and signaling mechanisms involved in chon-drogenic differentiation of MSCs.
The effect of bovine colostrum products on intestinal dysfunction and inflammation in a preterm pig model of necrotizing enterocolitis

The effect of bovine colostrum products on intestinal dysfunction and inflammation in a preterm pig model of necrotizing enterocolitisNecrotizing enterocolitis (NEC), primarily seen in preterm infants, is associated with high morbidity and mortality. The pathogenesis is not fully understood but risk factors include prematurity, enteral feeding (especially with milk formula), and the intestinal microbiota. Mother’s milk, rich in bioactive factors, has a protective effect against NEC, but not all preterm infants are able to receive mother’s milk. The overall aim of this thesis was to investigate if bovine colostrum (BC), also rich in bioactive factors, could serve as an alternative to mother’s milk. A preterm pig model of NEC was used to investigate the effect of BC products on intestinal structure, digestive and absorptive functions, microbiota, plasma and tissue proteins and tissue gene expression levels of inflammatory markers. In Study I, the aim was to investigate if BC could correct intestinal dysfunction and reduce inflammation induced by total parenteral nutrition (TPN) combined with an abrupt transition to milk formula, which has shown to initiate detrimental intestinal responses. A group of preterm pigs fed milk formula followed by BC was compared with groups of preterm pigs fed either milk formula or BC alone after the TPN period. This study showed that BC feeding restores intestinal dysfunction and reduces a proinflammatory response induced by short term (6 hours) formula feeding to preterm TPN-fed pigs. A prerequisite for the use of BC in clinical settings is that a standardized product is readily available, and in Study II it was investigated if pasteurized and/or spray dried BC had similar beneficial effects on intestinal dysfunction and inflammation as fresh BC. Preterm pigs were given TPN for two days followed by 6 hours of formula feeding before given either formula, BC, spray dried BC, or pasteurized and spray dried BC. The study showed that even though spray drying and pasteurization affected BC proteins, pasteurized and/or spray dried an in vitro model for the premature pig intestine. investigated if diet-induced effects could be observed on the expression of 48 epithelial- and immune response-related IPEC-J2 with formula, or growth medium. Distal samples from preterm milk formula or colostrum were included for comparison. careful considerations must made prior to
NEW RECORD OF INDONESIAN PIGFISH, BODIANUS IZUENSIS ARAGA AND YOSHINO, 1975, AND B. MASUDAI ARAGA AND YOSHINO, 1975 (PERCIFORMES: LABRIDAE), FROM NORTH SULAWESI, INDONESIA

One specimen of Bodianus izuensis Araga and Yoshino, 1975, and three specimens of B. masudai Araga and Yoshino, 1975, were obtained from fish markets in Bitung and Kema, Minahasa, North Sulawesi, Indonesia, between Marchâ€“July 2009. The specimens were caught from depths of about 20â€“30 m at coral reef ecosystem around Lembeh Island and Kema. This is the first record of these species in Indonesian waters. Morphological features, diagnostic characters, and distribution are discussed and illustrated, and color photographs of the species are presented.
Assessment of Seasonal Metabolic Acclimation in Gopher Tortoises (Gopherus polyphemus): Does Dormancy Reduce Metabolic Rate?

Environmental selective pressures, and associated constraints (such as sub-optimal thermal environments), imposed on organisms can drive important changes in energy usage in organisms exposed to the environmental constraints. Gopherus polyphemus, Gopher Tortoises, significantly reduce constitutive immunity during winter dormancy, a pattern that has been observed across ectothermic vertebrates. Herein, we assessed the metabolic consequences of winter acclimation to determine if the previously documented seasonal immune reduction confers measurable energy conservation. We measured oxygen (O2) consumption, carbon dioxide (CO2) production, and calculated respiratory quotient in G. polyphemus at two seasonally relevant temperatures (12.5°C and 32.5°C) and two seasonal acclimation states (winter and summer). We found no effect of season on either O2 consumption or CO2 production but found that RQ was significantly elevated in animals at the colder temperature (P < 0.001). Additionally, we found very high RQs (>1.0) in cold-acclimated animals during dormancy. High RQs in this species were likely a result of anaerobic digestive gases exiting the gastrointestinal tract, as we documented significant anaerobic carbon dioxide production in freshly collected fecal samples. Respiratory quotients were all below 1.0 and within normal ranges for vertebrates when a standardized mass-specific fecal CO2 enrichment was removed from total CO2 production. Oxygen consumption was greatest in animals at the warmer temperature, and the Q10 for O2 consumption in animals in this study was 2.34. While we failed to document a pattern of reduced temperature-independent metabolism during dormancy, results from this study further demonstrate important physiological modulation between dormancy and activity in this species of conservation concern.
The value of objective online measurement technology: Australian red meat processor perspective

In the past, the adoption of online measurement technologies for measuring carcass and meat quality traits objectively has been low among Australian red meat processors. The aim of the present work was to obtain a greater understanding of Australian processor views on the value of objective online measurement technologies. This was achieved through consultation with 65 Australian processors, to understand which carcass and meat quality traits they considered important to objectively measure and what they thought of current and future technologies. It was shown that beef processors ranked meat colour and tenderness as the most important traits (P < 0.001) to objectively measure online. Sheep processors ranked tenderness, pH, age, meat colour, total tissue depth at the 12th rib 110 mm from the midline (GR) and saleable meat yield percentage as the most important traits (P < 0.001) to objectively measure online. The overall processor responses indicated that there is support for online measurement technologies, with 80% of processors stating that online objective grading systems have a role in the Australian meat processing sector now and 88% considered these to have a role in the future. Much can be learned from the implementation of previous online objective measurement technologies by processors in terms of commercialisation and adoption strategies. The development and adoption of objective online measurement technologies is challenging and complex. However, increased adoption of online measurement technologies has the potential to achieve benefits to the whole of industry and needs continued support, coupled with new approaches to enhance adoption.
Pollination-Induced Gene Changes That Lead to Senescence in Petunia × hybrida

ii Acknowledgments. v Vita . vii List of Tables . xv List of Figures . xvi Chapter 1: Introduction . 1 Plant hormones . 2 Ethylene . 2 Abscisic acid . 3 Auxin . 4 Cytokinin . 5 Gibberellin . 5 Jasmonic acid . 6 Salicylic acid. 6 x Sugars . 7 Fatty acids . 8 Calcium . 9 Transcription factors and hormone cross talk . 9 Chapter 2: An optimized protocol to increase virus-induced gene silencing efficiency and minimize viral symptoms in petunia . 13 Abstract . 13. 13 Introduction . 14 Materials and methods . 17 Plant materials and growing conditions. 17 Plasmid construction. 18 Inoculum preparation . 19 Inoculation methods . 19 Cultivar optimization . 20 Temperature optimization. 20 Seedling age at inoculation . 21 Control construct evaluation and RT-qPCR expression analysis . 21 Growth chamber to greenhouse transition . 22 Gene silencing phenotypic evaluations . 23
Differential Effect of Weight Loss on Adipocyte Size Subfractions in Patients With t ype 2

The size of adipocytes influences their function suggesting a differential responsiveness to intervention. We hypothesized that weight loss in patients with type 2 diabetes mellitus (T2DM) predominantly decreases the size of large and very-large adipocyte subfractions in parallel with beneficial changes in serum adipokines and improved insulin sensitivity. A total of 44 volunteers from the Look Action for Health in Diabetes trial, who lost weight after 1-year of intense lifestyle intervention, were included. Insulin sensitivity (hyperinsulinemic–euglycemic clamp), size of subcutaneous abdominal adipocytes (osmium fixation), and selected serum adipokines were measured. A 13% weight loss was accompanied by 46% improvement in insulin sensitivity (increased glucose disposal rate from 5.9 ± 2.2 to 8.6 ± 2.7 mg/min/kg fat-free mass, P < 0.05) in parallel with a 36% increase in plasma adiponectin concentration (6.1 ± 3.1 to 8.3 ± 3.9 µg/ml, P < 0.05], but no changes in the proinflammatory cytokines interleukin-6 and tumor necrosis factor-α. Change in adiponectin correlated with changes in glucose disposal rate (r = 0.34, P < 0.05). Mean adipocyte size decreased (0.84 ± 0.25 to 0.64 ± 0.23 μl, P < 0.05), mainly due to changes in the large adipocyte subfraction (size 0.75–0.44 µl, relative number 19–26%; P < 0.05). Our data suggest that change in the large adipocyte subfraction may contribute to the improvement in insulin sensitivity via an increase in serum adiponectin. Such a relationship, which does not imply cause and effect, could not be obtained by measuring only mean adipocyte size. These data provide support for the measures of adipocyte size distribution in concert with in vitro adipokine secretion and lipolysis in future studies.
Salt and drought stress affects electron transport chain genes in rice

Article history: Received 5 July 2016 Received in revised form 21 October 2016 Accepted 10 November 2016 Rice is well known as a salt and drought sensitive crop. Salt and drought stresses greatly affect the growth and productivity of rice plants. To study the molecular response of rice to these abiotic stresses, 14 day-old whole seedlings of the MR253 rice variety were subjected to varying duration of droughtand salt-stress treatments. Using the Differential Display Reverse Transcription Polymerase Chain Reaction (DDRT-PCR), two putative genes were identified; one encodes the apocytochrome f precursor while the other codes for the ATP synthase B chain. The expression of the apocytochrome f precursor was downregulated by 10-fold compared to that of the untreated seedlings after one day of drought-stress treatment but its expression seemed to recover back up to levels similar to those of the untreated seedlings if the duration of drought stress was extended for more than one day. On the other hand, the ATP synthase B chain showed a two-fold increase in expression relative to that of the untreated seedlings after one hour of saltstress treatment but the level of its expression dropped back to those similar to the untreated seedlings if the duration of salt stress went beyond one hour. These findings suggest that genes encoding the apocytochrome f precursor and the ATP synthase B chain seem to play a role in the early molecular response of rice plants to abiotic stresses.
Isolation and screening of mucus-associated bacteria of the gastropod, Drupa margariticola for antagonistic activity

The mucus-associated bacteria of the gastropod, Driipa ~nargariticola were screened for their ability to inhibit the human and fish pathogens. Out of the two hundred and eighty five bacterial strains isolated, 23% (65) were found to be pigmented, 71% (202) were identified as Gram-negative. A higher percentage of nonpigmented (77%) and Gram-negative (71%) strains were observed in the present investigation. 16% (46) of the isolates was found to have antagonistic activity against both human and fish pathogens tested and 63% of the Gram-negative strains (29) were found to be antibiotic producers. Antagonistic activity was found to be exhibited by pigmented strains too. A higher degree of inhibition was conferred by 3 of the isolates (Dl,, Dl,, and D,,,) against both human and fish pathogens. These strains exhibited full or complete degree of inhibition against Eschericl~ia roli.
Tafazzin regulates human conjunctiva epithelial cell proliferation via inhibiting TGFβ signaling pathway

Purpose: To investigate the role of Tafazzin (TAZ) protein in regulating the proliferation of normal human conjunctiva epithelial cells and epithelial cells from pterygium tissue. Methods: Conjunctiva epithelial cells were cultured in keratinocytes growth medium and treated with transformation growth factor β (TGFβ) to analyze the expression and translocation of TAZ protein by immunostaining and BrdU analysis. Immortalized conjunctiva epithelial cells (NHC) were treated with TGFβ, targeting siRNA, TGFβ receptor antibody or TGFβ receptor inhibitor, to study the involvement of TAZ and TGFβ signaling pathway in conjunctiva cell proliferation by cell adhesion assay. Conjunctiva tissues from a normal human eye and an eye with pterygium disease were collected for histological analyses and western blot to evaluate the TAZ protein expression in vivo. Results: TAZ expression was upregulated in mitotic conjunctiva epithelial cells, proliferating conjunctiva epithelial cells, TGFβ treated conjunctiva epithelial cells and human pterygium epithelium. TAZ siRNA induced less conjunctiva epithelial cell growth. Moreover, TGFβ receptor antibody and TGFβ receptor inhibitor rescued this anti-proliferative effect of TAZ siRNA. Conclusions: TAZ is involved in human conjunctiva epithelial cells proliferation via regulating TGFβ signaling pathway.
Prevalence of aadA1, aadA2, aadB, strA and strB genes and their associations with multidrug resistance phenotype in Salmonella Typhimurium isolated from poultry carcasses

This study aimed to assess the prevalence of aminoglycoside resistance genes in S. Typhimurium isolated from poultry carcasses in Iran, and to reveal the most prevalent patterns of antimicrobial resistance. A total number of 300 samples of poultry carcasses were analyzed. Salmonella was isolated from 245 samples (81.66%). Multiplex PCR showed that 56.3% of the samples belonged to serovar S. Typhimurium and the remainder (43.6%) contained the rest of serovars. The highest rate of drug resistance was observed for tetracycline (97.0%), nalidixic acid (87.0%) and amoxicillinclavulanic acid (67.4%). These serovars, however, were sensitive to cefotaxime (84.8%), sulfamethoxazole trimethoprim (77.6%) and gentamicin (71.0%). aadA1 gene was detected in 63 isolates (45.6%), aadA2 in 48 isolates (34.7%), aadB in 43 isolates (31.1%), strA in 52 isolates (37.6%) and strB in 31 isolates (22.4%). High prevalence of aminoglycoside resistance genes in S. Typhimurium was shown. Furthermore, there was a significant association (P < 0.02) between the presence of aadA1, aadA2, strA and strB genes and resistance to streptomycin. Also, there was a significant association (P < 0.001) between the presence of aadB gene and resistance to kanamycin and gentamicin.
Fatty acids as cancer preventive tools in the dietary modulation of altered lipid profiles associated with hepatocarcinogenesis

Changes in lipid metabolism were monitored in rat hepatocyte nodules at certain time points over 9 months. Tissue obtained from partially hepatectomised rats collected over a period of 7 days, were included as a control for normal hepatocyte cell proliferation. Two important features regarding the lipid profiles of hepatocyte nodules and normal regenerating liver were the increased concentrations of phosphatidylethanolamine (PE) resulting in a decreased phosphatidylcholine/ phosphatidylethanolamine (PC/PE) ratio, and an increase in cholesterol. These changes coincided with increased membrane fluidity in the nodules and regenerating liver. With respect to the fatty acid (FA) profiles of the nodules, C18:1Τ9 and C18:2Τ6 increased in PE and PC whereas C20:4Τ6 decreased in PC and increased in PE. C22:5Τ6 and C22:6Τ3, the end products of the Τ6 and Τ3 metabolic pathways respectively, decreased in PC and remained unchanged in PE. The FA levels in PC reflected an impaired delta-6 desaturase enzyme, whereas this effect was masked in PE due to the increased concentration of this phospholipid fraction. In regenerating liver, the FA profiles of PC and PE showed the same pattern as described for the hepatocyte nodules, except for C18:1Τ9 which decreased in PC and increased nonsignificantly in PE. The increased C18:1Τ9 level, a FA with antioxidative properties, as well as the decreased levels of the long-chain polyunsaturated fatty acids (C20 and C22 carbon chains), have been associated with the decreased lipid peroxidation level in hepatocyte nodules. The resultant decrease in peroxidative metabolites, known to affect apoptosis, could be important in the progression of the nodules into neoplasia. The present results indicated that the altered lipid parameters associated with hepatocyte nodules closely mimics cellular proliferation in regenerating liver and could be responsible for the enhanced proliferation and/or altered growth pattern in these lesions. The altered FA profiles, especially the increased level of C20:4Τ6 in PE, suggest various pathways in which FA could play a role in transmembrane signaling related to the altered cell proliferative and apoptotic pathways. The persistent changes in the hepatocyte nodules suggest that the lipid metabolism escapes the regulatory mechanisms required for normal cellular homeostasis at different levels.
Is the body condition of the three-spined stickleback (Gasterosteus aculeatus) determined by the type of food consumed?

Abstract The three spine stickleback Gasterosteus aculeatus is a small omnivorous, wildly distributed fish. In this study, food uptake and body condition of three spine stickleback, from the Gulf of Gdansk eulitoral was investigated. Samples were taken from three locations of the Gulf of Gdańsk: in vicinities of Sopot, Chałupy and Hel. Copepods were the most quantitive food components in the three spine stickleback stomachs. In spring, at Hel station -Harpacticoida and in Sopot, crustacean and fish eggs, were dominating as a fish prey. During summer, Calanoida were most abundant in stomachs collected from fish caught in Chałupy, fish eggs and Calanoida in those from Hel station. In stomachs of fish from Sopot location most common prey were Cladocera. Comparison of stomach content to food base and Fulton’s body condition index revealed that the three spine stickleback uses available food base in efficient way.