Miracle-dz/UniFAR-FTUs huggingface dataset:
Zebrafish vps33b, an ortholog of the gene responsible for human arthrogryposis-renal dysfunction-cholestasis syndrome, regulates biliary development downstream of the onecut transcription factor hnf6

Arthrogryposis-renal dysfunction-cholestasis syndrome (ARC) is a rare cause of cholestasis in infants. Causative mutations in VPS33B, a gene that encodes a Class C vacuolar sorting protein, have recently been reported in individuals with ARC. We have identified a zebrafish vps33b-ortholog that is expressed in developing liver and intestine. Knockdown of vps33b causes bile duct paucity and impairs intestinal lipid absorption, thus phenocopying digestive defects characteristic of ARC. By contrast, neither motor axon nor kidney epithelial defects typically seen in ARC could be identified in vps33b-deficient larvae. Biliary defects in vps33b-deficient zebrafish larvae closely resemble the bile duct paucity associated with knockdown of the onecut transcription factor hnf6. Consistent with this, reduced vps33b expression was evident in hnf6-deficient larvae and in larvae with mutation of vhnf1, a downstream target of hnf6. Zebrafish vhnf1, but not hnf6, increases vps33b expression in zebrafish embryos and in mammalian liver cells. Electrophoretic mobility shift assays suggest that this regulation occurs through direct binding of vHnf1 to the vps33b promoter. These findings identify vps33b as a novel downstream target gene of the hnf6/vhnf1 pathway that regulates bile duct development in zebrafish. Furthermore, they show that tissue-specific roles for genes that regulate trafficking of intracellular proteins have been modified during vertebrate evolution.
Genetic diversity and gene flow in Clarias gariepinus from Lakes Victoria and Kanyaboli, Kenya

The African catfish Clarias gariepinus is an important species in the rapidly expanding aquaculture industry in East Africa. Most Kenyan catfish farmers use stocks with unknown genetic characteristics, with uncertified seeds and inter-basin exchange of brood stocks threatening the genetic distinctness of wild populations. Using 346 base pairs of D-loop sequence variation, genetic diversity and gene flow between C. gariepinus populations from Lake Victoria and its satellite, Lake Kanyaboli, were explored. A total of 17 haplotypes were identified in 52 individuals sampled, with the two populations sharing four haplotypes, and one haplotype being the most frequent (50%) in both populations. Catfish from Lake Victoria showed marginally higher genetic variation compared to those from Lake Kanyaboli, reflected in the higher number of haplotypes, singletons, polymorphic sites and haplotype and nucleotide diversities. Yet neither population showed signs of significant loss of diversity compared to other wild populations of the species. Clarias gariepinus from Lakes Victoria and Kanyaboli clustered into one clade, showing low population structuring and with a between-population FST value of 0.026, which was not indicative of significant (p ≥ 0.05) differentiation between the two lakes. Nevertheless, each population contained 60–64% of unique haplotypes. Inter-basin transfer of Clarias populations and human impact on Lake Kanyaboli should be controlled to conserve the unique Clarias genetic resources in the lake basin of Kenya.
An Indirect Quantitative Fluorescence Immunoassay for the Detection of Lyme Disease Serum Antibody

Determination of serum antibody levels to Borrelia burgdorferi is often helpful in the diagnosis of Lyme disease. Established procedures include the indirect fluorescent antibody (IFA) and enzyme-linked immunosorbent assay (ELISA). ’-3x5 In this study an indirect quantitative fluorescence immunoassay (FIAX) was evaluated. A total of 247 sera were tested by FIAX and the conventional IFA test, including 46 normal individuals from a nonendemic area (Maryland), 147 patients meeting case definition (presence of erythema migrans, EM), and 54 patients with other spirochetal or autoimmune diseases. In addition, 50 sera from individuals residing in an endemic area (Northern Wisconsin) and 72 patients with neurologic disease were tested by FIAX alone.
Dispersion of Drosophila pseudoobscura

In a recent paper, Wallace (1966) re-examined data on the dispersion of Drosophila pseudoobscura reported by Dobzhansky and Wright (1943). He found that "the log of the number of flies recaptured at various distances from the point of release (both for capture of individual days following release and, for practical purposes, the cumulative captures of all days) decreases linearly with the square root of the distance. " There is serious inconsistency with the results of the 1943 analysis, which is not immediately obvious and not referred to by the author. In each of four experiments (I-IV), several thousand orange-eyed flies were released at the center of a cross-shaped array of traps, 20 m apart, in an area inhabited by wild red-eyed flies of the same species. The numbers of both sorts, caught in the traps, were recorded daily. The flies dispersed so widely that it became necessary on the second or third day to drop two arms of the cross in order to extend the others. After demonstrating that temperature was a major cause of differences in activity, both in percentage trapped and amount of dispersion, an attempt was made to obtain some idea of the nature of the dispersion for each day in each experiment by calculating the kurtosis. The formula used was
Development and application of direct immunofluorescence assay for detection of porcine reproductive and respiratory syndrome.

A direct immunofluorescence assay (FA) was developed for the detection of porcine reproductive and respiratory syndrome virus (PRRSV) using fluorescein isothiocyanate (FITC) labeled immunoglobulin (IgG). Virus antigens in cell culture monolayer and tissue sections and virus propagation dynamics in MARC-145 cells was detected by the FA. The results showed that the antigen positive cells could be detected from 16 h PI, and virus propagation peaked at 60 h to 72 h PI. Antigen positive cells was found in inguinal lymph nodes, jejunum, testis, spleen, mandibular lymph nodes, mesenteric lymph nodes and tonsil, respectively. The clinical samples from 38 cases of affected pigs were evaluated using the FA, and 63.2 % (24/38) was detected PRRSV positive. The assay was sensitive, specific and reproducible, and showed 96.3 % consistence with RT-PCR detection.
Optimizing Hardwood Reforestation in Old Fields: The Effects of Treeshelters and Environmental Factors on Tree Seedling Growth and Physiology

Strong competition for water is largely recognized as the main factor explaining the resistance of herbaceous old fields to tree invasion. Therefore, site preparation as well as chemical and mechanical vegetation control are recommended when establishing hardwood tree plantations on such sites, but those methods are sometimes socially or ecologically inappropriate. The main objective of this study was to analyze whether treeshelters could improve early tree growth in herbaceous old fields, when mulching alone is used to partially control herbaceous competition. Our results indicate that treeshelters can facilitate tree growth in those conditions but that this was not caused by an improvement of tree water relations. Rather, it appeared to be related to an optimization of light levels inside the shelter, where light intensity was low enough to lead to a photosynthetic system less costly to maintain due to a greater specific leaf area but high enough to have no adverse effects on photosynthetic rates. Although treeshelters increased tree growth when surrounding herbaceous vegetation was low (either height or standing biomass), allowing high light levels, they reduced growth when surrounding vegetation was high and blocked a substantial quantity of light. Therefore, environmental factors such as light availability need to be considered to optimize the success of hardwood plantations when treeshelters are used in recently abandoned agricultural fields.
Impact of insect herbivores on competition between birds and mammals for pinyon pine seeds

Few studies have considered impacts of insect cone herbivores on bird and mammal seed consumers. Harvests of pinyon pine (Pinus edulis) cones by insects, birds, and mammals were negatively correlated both within and across sites. Birds and mammals significantly increased their cone harvest when the other group was experimentally pre- vented access to trees, and mammals harvested more cones when insects were removed from trees with an insecticide. These results suggest that stem- and cone-boring insects (primarily Dioryctria albovittella), birds (Clark's Nutcrackers, Pinyon Jays, and Scrub Jays), and mammals (cliff chipmunks and rock squirrels) compete for pinyon pine seeds. Addi- tionally, insects affected the interaction between birds and mammals because the ratio of mammal to bird harvest increased up to 350-fold as insect cone consumption increased. Because insect-infested and uninfested pinyon pines are genetically different, these obser- vations and experiments suggest that genetic interactions between plants and herbivores can affect the structure of a seed-consumer community.
Accumulation of a Metallothionein‐like mRNA in Norway Spruce Under Environmental Stress

Differential screening of a Norway spruce (Picea abies L., Karst) cDNA library with probes from damaged and symptomless trees identified a cDNA clone of a 650 nt metallothionein-like (MTL) mRNA as damage-related. Northern blot analysis revealed an about six-fold increase of the MTL mRNA in damaged trees in 1 year and a two-fold increase in the consecutive year. In the N-terminal domain this MTL mRNA comprises typical CysXCys motifs of a subgroup of class II MTL proteins found in kiwi and a few other plant species. In the C-terminal domain, however, the Norway spruce MTL protein is different to the kiwi subgroup and also distinct from a novel Douglas fir metallothionein-related protein, respectively. Hence, the cDNA identified during this study may represent a new type of MTL protein in plants. The accumulation of this MTL mRNA in needles of trees growing in an area of high ozone, sulphur dioxide and nitrogen oxide input and showing clear symptoms of forest decline may be a senescence effect or may play a role in the metal-mediated regulation of the intracellular activated oxygen concentration. Zusammenfassung Differentielles Screening einer cDNA-Bank aus Fichte (Picea abies L. Karst) mit Sonden aus geschadigten und symptomlosen Baumen identifizierte eine 650 nt lange Metallothionin-ahnliche (MTL) mRNA als schadenskorreliert. In Northernblot-Analysen konnten in Juliproben zweier aufeinanderfolgender Jahre ein sechsfacher und ein zweifacher Anstieg der MTL-mRNA nachgewiesen werden. Im N-terminalen Bereich weist dieses Protein typische CysXCys-Motive einer Untergruppe von Klasse II-MTL-Proteinen aus Kiwi und einigen anderen Pflanzen auf. In der C-terminalen Region weicht das MTL-Protein aus Fichte jedoch von dieser Untergruppe ab und ist auch verschieden von einem neuartigen Metallothionin-verwandten Protein aus der Douglasie. Daher handelt es sich vermutlich um einen neuen Typ eines MTL-Proteins in Pflanzen. Die erhohte Expression des MTL-Proteins in Fichten aus einem Gebiet mit hohem Ozon-, Schwefeldioxid-und Stickoxid-Eintrag und mit den typischen Symptomen der neuartigen Waldschaden mag ein Seneszenzeffekt sein oder eine Rolle spielen in der Metallionen-vermittelten Regulation der Konzentration aktivierten Sauerstoffs in der Zelle.
Battus polydamas (Lepidoptera: Papilionidae) Uses the Open-Field Aristolochia sessilifolia (Piperales: Aristolochiaceae) as Its Host Plant in Uruguayan Savanna Areas

Abstract Butterfly species with broad geographical ranges are expected to be tolerant of ecological/ environmental constraints and to shifts in host plant use. This seems to be the case of the butterfly Battus polydamas (Linnaeus, 1758) (Lepidoptera: Papilionidae), which in the absence of better host plants may lay eggs on low-quality Aristolochia (Piperales: Aristolochiaceae) plants, increasing the developmental time and mortality rate of immatures. Battus polydamas populations from the Uruguayan savanna were investigated to verify whether A. sessilifolia (Klotzsch) Duch. was being used as a host plant in grassland areas where no other Aristolochia species are available. Species distribution models (SDM) for both species were built to verify whether ecological conditions could cause overlapping distributions between them. Extensive field surveys were performed to investigate whether B. polydamas actually uses A. sessilifolia as larval food source in the field. The performance of larvae on such host plant was also tested under controlled conditions in a laboratory environment. The SDM analysis showed a large overlap between the distributions of B. polydamas and A. sessilifolia. Field surveys revealed the occurrence of an interaction between the butterfly and the potential host plant, and laboratory experiments corroborated that B. polydamas larvae can successfully use A. sessilifolia as a host plant. The wide distribution of B. polydamas suggests that this butterfly species evolved the ability to develop in unfavorable environments (e.g., poor host plants, adverse climate), allowing it to use virtually all Aristolochia species of the Neotropics as host plants. Thus, adult females appear to have developed the capacity to identify any Aristolochia spp. as a suitable host plant, enabling the exploitation of various landscapes and ecoregions.
Acid hydrolysis of kappa-carrageenan as a way of gaining new substances for freezing process modification and protection from excessive recrystallisation of ice

Summary The effects of κ-carrageenan and its hydrolysates on modification of the freezing process and also on inhibition of excessive recrystallisation of ice in sucrose solutions during storage were compared. Acid hydrolysis of κ-carrageenan was carried out using sulphuric (H2SO4) and hydrochloric acid (HCl). Most effective in the hydrolysis process turned out to be H2SO4, which degraded κ-carrageenan to a molecular mass of around 3 × 106 Da, after 1.5 h of hydrolysis. Addition of 0.005% of the new poligeenan (degraded carrageenan), to a sucrose solution (30%), frozen at −20 °C, caused a nearly 50% reduction in the phase-change stages, and consequently, the total time of freezing was shorter. Significant retardation of recrystallisation was observed for both types of poligeenan, but a stronger effect was observed for the oligosaccharides obtained after HCl hydrolysis, and after 96 h of storage at −8 °C, the equivalent diameter of ice crystals was not greater than 11 μm.
Repair of chronic type 1 dissection in a patient with coronary artery anomaly

ÖZ Akut tip 1 diseksiyonda olgular asemptomatik olsa dahi, cerrahi tedavi en önemli tedavi seçeneği olarak düşünülmesine rağmen, kronik asemptomatik olgularda cerrahi tedavi kararı için çıkan aortun çapı önem arz etmektedir. Bu yazıda, sol ana koroner arterin sağ koroner sinüsten çıktığı kronik tip 1 diseksiyonu olan 50 yaşında bir erkek olgu sunuldu. Akut tip 1 diseksiyon muhtemelen iki ay önce gelişmişti ve pulmoner ödem ile yanlış tanılanmıştı. Ameliyat sırasında arkus aorta proksimal seviyesinde diseksiyon flep fenestrasyonu, tek buton reimplantasyonu ile Bentall işlemi ve sol ön inen koroner arter-sol internal torasik arter anastomozu yapıldı. Sorunsuz ameliyat sonrası dönemi takiben, hasta tam şifa ile 10. günde taburcu edildi. Anah tar söz cük ler: Aort diseksiyonu; koroner damar anomalisi; cerrahi; fenestrasyon. ABSTRACT Although surgical intervention is considered to be the most appropriate therapeutic choice for acute type 1 dissection even in asymptomatic cases, the diameter of ascending aorta is critical for decision in chronic asymptomatic cases. In this article, we report a 50-year-old male case of chronic type 1 dissection with left main coronary artery originating from the right coronary sinus. Acute type 1 dissection probably occurred two months ago and the patient was misdiagnosed with pulmonary edema. During surgery, the dissection flap fenestration at the level of proximal aortic arch, the Bentall procedure with one button re-implantation, and the left anterior descending coronary artery-left internal thoracic artery anastomosis was done. After an uneventful postoperative period, the patient was discharged with full recovery on the 10th day.
Influence of repair proteins and chromatin modifiers on mobility of DNA double-strand breaks induced by heavy ion irradiation

Ionizing radiation induces DNA double strand breaks (DSBs) in cell nuclei which represent the most dangerous type of DNA lesions. Through error prone repair mechanisms they can lead to the formation of chromosome rearrangements, favoring genomic instability and the development of cancer. Movement of DSBs and surrounding chromatin domains is expected to influence DSB repair and promote the formation of chromosomal translocations. Addressing this expectation, DSB mobility was analyzed after heavy ion irradiation. To gain insight into influences of chromatin organization and repair related factors on the dynamic behavior of DSB sites, knockdown or inhibition of repair proteins and chromatin modifying proteins was used. Occurring changes in irradiation induced foci (IRIF) mobility were examined either by immunofluorescent analysis of fixed samples or by live cell microscopy.
Enhanced biobutanol production using novel clostridial fusants in simultaneous saccharification and fermentation of green renewable agriculture residues

Thermostable Clostridia species were developed in the present study through protoplast fusion between mesophilic and thermophilic clostridial species. Two parental strains of Clostridia species, Clostridium acetobutylicum (ATCC 4259) and Clostridium beijerinckii (ATCC BA101), along with three fused strains, Clostridium acetobutylicum Clostridium thermocellum (CaCt), Clostridium beijerinckii Clostridium thermocellum (CbCt) and Clostridium acetobutylicum Clostridium beijerinckii (CaCb), were examined for biobutanol production using wheat straw (WS) as a feedstock in a batch process of simultaneous saccharification and fermentation (SSF). The objective of the study was to use the thermotolerant fused strains to enhance enzymatic activity during the SSF by raising the incubation temperature and thereby eventually increasing biobutanol production. Results from the current study indicated that the fused strains were able to produce the required enzymes at higher temperature essential for the saccharification of WS (i.e., endoglucanase, exoglucanase, and β‐glucosidase). This will have a major impact on eliminating costs associated with adding enzymes to the saccharification process. Fused strain CbCt achieved the highest biobutanol production of up to 14.13 g/L (i.e., a yield of 0.29) at 45 °C with total sugar consumption of 82%. Enzymatic activity of CbCt was found to be 61.67 FPU (filter paper unit) which was the highest in comparison with other fused strains evaluated in this study. These results indicate a breakthrough for the technological and economical obstacles associated with industrialization of the SSF process. © 2015 Society of Chemical Industry and John Wiley & Sons, Ltd
Temporal and depth distribution of microepiphytes on Posidonia oceanica (L.) Delile leaves in a meadow off Tunisia

A survey on the epiphytic microorganisms growing on Posidonia oceanica leaves was conducted along a depth transect along the coast of Eastern Tunisia (Mahdia). Samples were collected by SCUBA diving at depths of 3, 5, 10 and 12 m in July 2008 and January 2009. A total of 58 microepiphyte taxa were identified. Multivariate analyses revealed temporal and spatial variation of the abundance of epiphytic microalgae. Water motion, light availability, temperature and motility of species seem to be responsible of temporal and bathymetric variations of epiphytic microalgae. Unlike diatoms, dinoflagellates were more abundant in deep waters, suggesting that they are more vulnerable to hydrodynamics. The significant correlation between leaf area index and abundance of epiphytic species indicates that the phenological parameters of the host plant influence the abundance of the epiphytic microorganisms. Among the epiphytic dinoflagellates, our data showed a great number of potentially toxic species (Alexandrium minitum, Amphidinium carterae, Karenia selliformis, Coolia monatis, Karlodinium veneficum, Ostreopsis siamensis, Prorocentrum concavum, Prorocentrum minimum, Prorocentrum rathymum and Prorocentrum lima). These species were more abundant in the deep station under more sheltered conditions than found at inshore shallower stations, which are subjected to high water motion.
Studies on genetic variability, heritability and genetic advance in cucumber (Cucumis sativus L.)

The experiment was conducted in Randomized Block Design with three replications to assess the performance of 27 genotypes of cucumber to determine nature of variability, character association, path analysis and genetic divergence. Observations were recorded on 12 quantitative characters viz., days to first male flower anthesis, days to first female flower anthesis, node number to first staminate flower appearance, node number to first pistillate flower appearance, number of primary branches per plant, vine length (m), days to first fruit harvest, fruit length (cm), fruit diameter (cm), number of fruit per plant, average fruit weight (g), fruit yield per plant (kg). The analysis of variance revealed significant differences among the genotypes for all the characters except days to maturity. Based on mean performance most promising genotypes viz., NDCC-7, NDCC-15, JPCC-1, JPCC-4 were found as most promising genotypes for high yield per plant. The estimates of phenotypic coefficients of variation (PCV) were higher than genotypic coefficients of variation (GCV) for all the characters. The highest phenotypic as well as genotypic coefficients of variation were observed in number of primary branches followed by fruit length. High heritability coupled with low genetic advanced in per cent of mean were observed for fruit length followed by days to first male flower anthesis, number of primary branches, average fruit weight, node to first male flower anthesis had exhibited highly significant and positive phenotypic correlation with number of fruit per plant followed by vine length, fruit diameter, number of primary branches per plant, days to first male flower anthesis, days to female flower anthesis and fruit length.