Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Fat and Fat Free Live Weight in Broiler Chickens Using Backskin Fat, Abdominal Fat, and Live Body Weight

Abstract Data from 100 male and 100 female broiler chickens that were raised on the floor under two lighting regimes (12 and 24 hr light) were combined. Birds were weighed when 58 days old (male data presented first) (2372 g, 1913 g) and then slaughtered at 59 days. Abdominal fat was weighed (2.18%, 2.82%) and fat extracted from ground carcass (12.0%, 13.7% wet basis), intestines (47.6%, 56.2% dry basis), and from a triangular section of backskin (86.1%, 88.0% dry basis). Percent total fat was 10.4 and 12.2 (wet basis). Abdominal fat regressed on live body weight produced negative intercepts, indicating that regressed rather than percent values should be used. Fat from the four locations mentioned above had correlation coefficients of +. 45 to +. 76 for males and +. 47 to +. 74 for females. Percent abdominal fat had low nonsignificant correlations with fat free live body weight (r = +.23 male, −.07 female). Abdominal fat weight was a better (higher r2) predictor of total fat, total fat minus abdominal fat, percent carcass fat, and percent intestinal fat, than percent backskin fat. Thirty-three percent (male) and 22% (female) of the variation of percent abdominal fat was accounted for by percent backskin fat. Abdominal fat should be obtained directly and used for predicting fat in the bird rather than backskin fat. Abdominal fat was +20.7% (male) and +22.8% (female) of total fat. Prediction equations for estimating total fat and fat free live weight, given abdominal fat, and live body weight were developed. Selection against percent abdominal fat would probably result in a reduction of fat in other locations and little change in fat free live weight.
Role of Biogenic Amines in Oviposition by the Diamondback Moth, Plutella xylostella L

Oviposition is an important reproductive behavior that is triggered by mating in insects, and biogenic amines might be involved in its regulation. The effects of biogenic amines on oviposition have only been studied in a few insect species, and the findings to date have not been conclusive. In addition, there are few studies on the effects of biogenic amines on oviposition of the diamondback moth, Plutella xylostella L. Here, we tested how mating and biogenic amines regulate oviposition of P. xylostella by injecting amines and amine receptor antagonists into virgin and mated females and counting the number of eggs laid afterward. Biogenic amines of octopamine and tyramine could induce virgin adults of P. xylostella to lay eggs, while dopamine and serotonin had no such effect on oviposition. Furthermore, the octopamine antagonists mianserin, epinastine, and phentolamine inhibited oviposition by mated females. The tyramine antagonist yohimbine, dopamine antagonist SCH23390, and serotonin antagonist ketanserin did not block oviposition by mated females, and octopamine and tyramine-inducing oviposition by virgin females could be inhibited by the octopamine antagonists mianserin and epinastine instead of the tyramine antagonist yohimbine. We conclude that octopamine and its receptors are involved in mating-triggered oviposition in P. xylostella, while tyramine acts as a subsidiary. Further, the inducing effect of tyramine on oviposition is achieved via octopamine receptors instead of tyramine receptors. This experiment is helpful to further understand the role of biogenic amines in mating regulation and to provide a new strategy for controlling P. xylostella.
Ultrastructure and chemistryofepicuticular wax crystals in Polytrichales sporophytes

AbstractResults of scanning-electron-microscopic and chemical investigations of the epicuticular waxes on some Polytrichales spofophytes are presented. In Atrichum, Oligotrichum, Polytrichum, Pogonatum (Polytrichaceae) and Dawsonia (Dawsoniaceae) short Wax tubules were observed, corresponding to the epicuticular crystal shapes of most gymnosperms and some angiosperms. In some species they extend into helical appendices. The composition of cuticular Waxes on sporophytes of Pogonatum belangeri and P. urnigerum (n-alkanes, n-alkyl esters, n-alkanals, primary n-alkanols, and nalkanoic acids) closely resembles that of moss gametophytes and of higher plants. The dominating compound, nonacosan-10-ol, is shown to constitute the tubular Wax aggregates. Possible functional aspects of epicuticular Wax crystals on mosses and their convergent or original evolutionary character are discussed.
Ertragsstruktur alter und neuer Winterweizensorten unter dem Aspekt der Einlagerung und Remobilisation von Fruktanen im Weizenhalm

Yield components in old and new german winter wheat varieties with respect to the storage and remobilization of fructan in the wheat stem Yield components and changes in carbohydrate content of four old german winter wheat varieties, bred before 1950, were compared with six new varieties over two years in field trials. In both years the old varieties built up more biomass than the new varieties. In the latter a better harvest-index (0,56) as compared to the old varieties (0,43) was obtained, resulting in higher grain yields for the new varieties. Changes in water-soluble carbohydrate (WSC) content were mainly due to variations in fructan content. Maximum of fructan content was mostly reached at the stage of early milk ripeness. In the new varieties a faster and more complete remobilization of fructan occurred; especially in the year with the short grainfilling period.
Conservation genetics of regionally extinct peregrine falcons (Falco peregrinus) and unassisted recovery without genetic bottleneck in southern England

The peregrine falcon ( Falco peregrinus ) has been affected by persecution, pollution, trade, and habitat degradation, but it is considered a flagship conservation success story because of successful reintroductions and population recoveries across broad ranges. However, in the UK there were never formal reintroduction programmes for peregrine falcons, and it appears that UK populations—and specifically the Sussex peregrines of the English south coast—recently recovered from a population crash unassisted. To study this, we obtained samples from contemporary populations in southern England, Ireland, continental Europe, domestic-bred peregrine falcons, and from England pre-population crash. Using microsatellite and mtDNA control region data, the genetic diversity and structure, signatures of genetic bottlenecks, and potential origin of the Sussex peregrines was investigated. We found low levels of genetic diversity across all peregrine falcon groups, low but significant genetic differentiation, and a few private alleles, indicating some level of genetic structure among European peregrines. Although we could not pinpoint the origin of the Sussex peregrines, the data suggests that it is not likely to have originated from escaped domestic birds or from adjacent European populations. The results obtained here parallel other studies on peregrines elsewhere showing low genetic diversity but genetic structure. We conclude that not enough time elapsed for genetic erosion to occur due to the population bottleneck, and that at least for the Sussex peregrines there is no need for genetic conservation by wild-take and subsequent captive breeding programmes as long as current protection measures remain in place.
Mechanism of murine Vγ1+ γ δ T cell‐mediated innate immune response against Listeria monocytogenes infection

Murine γ δ T cells participate in innate immune response against infection of the intracellular bacterium Listeria monocytogenes. In the present report, we analyzed the mechanism of the γ δ T cell‐mediated response against L. monocytogenes infection. γ δ T cell‐enriched spleen cells of L. monocytogenes‐infected mice produced IFN‐γ in vitro in response to L. monocytogenes‐infected spleen cells. The IFN‐γ production was abrogated by depletion of Vγ1+ γ δ T cells. IFN‐γ production of the Vγ1+ γ δ T cells in response to L. monocytogenes‐infected spleen cells required IL‐12. However, addition of Fab fragment of anti‐TCR γ δ monoclonal antibodies (mAb) failed to block the response, suggesting that the response requires no TCR‐mediated antigen recognition. Interestingly, Vγ1+ γ δ T cells of naive mice also produced IFN‐γ in response to L. monocytogenes‐infected spleen cells in an IL‐12‐dependent manner. Furthermore, the IL‐12 receptor (IL‐12R) gene was expressed on the Vγ1+ γ δ T cells of naive mice as well as those of L. monocytogenes‐infected mice although naive α β T cells lack IL‐12R expression. All the results suggest that the Vγ1+ γ δ T cells participate in immune surveillance against intracellular bacterial infection through quick production of IFN‐γ in response to infection‐induced IL‐12 without antigen‐driven clonal expansion and maturation.
PHERI—Phage Host ExploRation Pipeline

Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multi-resistant bacterial strains occurring in all world regions. One of the possible future solutions is the use of bacteriophages in therapy. Bacteriophages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm based tool called PHERI. PHERI predicts suitable bacterial host genus for purification of individual viruses from different samples. Besides, it can identify and highlight protein sequences that are important for host selection. PHERI is available at https://hub.docker. com/repository/docker/andynet/pheri. The source code for the model training is available at https://github.com/andynet/pheri_preprocessing, and the source code for the tool is available at https://github.com/andynet/pheri.
S-phase-independent silencing establishment in Saccharomyces cerevisiae

The establishment of silent chromatin, a heterochromatin-like structure at HML and HMR in Saccharomyces cerevisiae, depends on progression through S phase of the cell cycle, but the molecular nature of this requirement has remained elusive despite intensive study. Using high-resolution chromatin immunoprecipitation and single-molecule RNA analysis, we found that silencing establishment proceeded via gradual repression of transcription in individual cells over several cell cycles, and that the cell-cycle-regulated step was downstream of Sir protein recruitment. In contrast to prior results, HML and HMR had identical cell-cycle requirements for silencing establishment, with no apparent contribution from a tRNA gene adjacent to HMR. We identified the cause of the S-phase requirement for silencing establishment: removal of transcription-favoring histone modifications deposited by Dot1, Sas2, and Rtt109. These results revealed that silencing establishment was absolutely dependent on the cell-cycle-regulated interplay between euchromatic and heterochromatic histone modifications.
Comparative chloroplast genomics between Euglena viridis and Euglena gracilis (Euglenophyta)

Bennett M.S., Wiegert K.E. and Triemer R.E. 2012. Comparative chloroplast genomics between Euglena viridis and Euglena gracilis (Euglenophyta). Phycologia 51: 711–718. DOI: 10.2216/12-017.1 The chloroplast genomes of Euglena gracilis, Eutreptia viridis, Eutreptiella gymnastica, Colacium vesiculosum, Strombomonas acuminata and the colourless Euglena (Astasia) longa, which had secondarily lost the ability to photosynthesize, were previously reported. These studies had shown that there was a great diversity in the size of euglenoid chloroplast genomes and in the arrangement of gene clusters. However, while these genomes provided important insights into the evolution of the chloroplast genome across genera, they did not address genomic variability within a genus. In an effort to continue with these investigations, we sequenced the chloroplast genome of Euglena viridis and compared this to the E. gracilis chloroplast genome in order to explore intrageneric chloroplast evolution. The chloroplast genome of E. viridis was also compared to those of the other previously published euglenoid chloroplast genomes. Our results showed that while the chloroplast genome of E. viridis most closely resembled that of E. gracilis, the chloroplast genomes did show significant differences. The chloroplast genome of E. viridis was far more compact, had a gene cluster that was reversed in both gene order and strand orientation, had a region that was comprised almost entirely of open reading frames and had substantially fewer introns. However, despite these differences, it was clear from the chloroplast genome sequence that E. viridis and E. gracilis were very closely related and that the majority of euglenoid chloroplast evolution probably occurred before the divergence of the genus Euglena.
Single Cell Transcriptomics-guided Antisense Treatment Improves Endoderm Differentiation of iPSCs

Directed differentiation of induced pluripotent stem cells (iPSCs) enables the production of relevant cell types for studies of human biology, disease-modeling, and efforts towards cellular therapy and transplantation. However, the low yield and purity of desired cell types can limit the utility of this approach. Enhancing differentiation purity can require extensive optimization of morphogen treatments, and this can still be ineffective for iPSC lines with biased or aberrant differentiation propensities. To address these limitations, we have developed a new approach for increasing the purity of iPSC directed differentiation cultures called RNA sequencing and Antisense-assisted Differentiation (RAD). We performed trajectory analysis of single cell RNA sequencing during iPSC differentiation into endoderm to identify transcription factors responsible for committing cells to undesired, non-endodermal fates. Specific suppression of these transcription factors using antisense oligonucleotides (ASOs) increased the percentage of endodermal cells by up to 20-fold in 3 different iPSC lines that exhibited poor endoderm differentiation. Moreover, this approach required minimal culture manipulation. Thus, RAD improves the utility of iPSCs for basic and translational studies.
Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation

During transcription initiation, the RNA polymerase holoenzyme (RNAP) and the promoter form an open complex. For many promoters, this interaction involves upstream DNA wrapping, downstream promoter bending, and associated large-scale protein rearrangements. Although these processes have been reported across the life kingdom, their structure, energetics, and role in transcription remain an area of active research. Using optical tweezers, we find that these processes become energetically and reversibly coupled after the formation of the open promoter complex, providing the main contribution to their stability. Using electron microscopy and single particle analysis, we find that the interaction encompasses from positions −76 to +18 along the template, that it involves an overall DNA bent angle of ~245°, and that the upstream wrapping is enabled by interactions between the C-terminal domains of RNAP’s alpha subunits and proximal and middle upstream promoter regions. The energy associated with upstream wrapping, downstream bending and its coupling to downstream rearrangements does not require specific upstream promoter sequence, and correlate positively with the rate of transcription DNA bubble formation as reported by a real-time fluorescence assay. Our results suggest that the coupling between upstream and downstream events are part of a cis-regulatory network established after the opening of the DNA bubble, that could furnish a control mechanism of gene expression by protein factors and regulatory metabolites. Summary The first step of gene expression involves transcription of DNA into RNA by RNA polymerase (RNAP). RNAP recognizes a promoter sequence forming the transcriptionally active open complex. For several promoters, DNA wraps around the RNAP. We find that upstream wrapping contacts are energetically coupled and occur cooperatively with downstream rearrangements in the open complexes, providing the largest contribution to their stability. We also determined that upstream wrapping is enabled by interactions between non-specific upstream promoter regions and RNAP α subunit C-terminal domains. Significantly, the strength of these contacts correlates with the rate of DNA bubble opening, and is regulated by factors such as the transcriptional regulator ppGpp. We suggest that any modulator altering upstream wrapping and downstream rearrangements could finely tune gene expression in response to the needs of the cell
Targeting of cholera toxin A (ctxA) gene by zinc finger nuclease: pitfalls of using gene editing tools in prokaryotes

Background and purpose: The study was launched to use zinc finger nuclease (ZFN) technology to disrupt the cholera toxin gene (ctxA) for inhibiting CT toxin production in Vibrio cholera (V. cholera). Experimental approach: An engineered ZFN was designed to target the catalytic site of the ctxA gene. The coding sequence of ZFN was cloned to pKD46, pTZ57R T/A vector, and E2-crimson plasmid and transformed to Escherichia coli (E. coli) Top10 andV. cholera. The efficiency of ZFN was evaluated by colony counting. Findings/Results: No expression was observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blotting in transformed E. coli. The ctxA gene sequencing did not show any mutation. Polymerase chain reaction on pKD46-ZFN plasmid had negative results. Transformation of E. coli Top10 with T/A vectors containing whole ZFN sequence led to 7 colonies all of which contained bacteria with self-ligated vector. Transformation with left array ZFN led to 24 colonies of which 6 contained bacteria with self-ligated vector and 18 of them contained bacteria with vector/left array. Transformation of V. cholera with E2-crimson vectors containing whole ZFN did not produce any colonies. Transformation with left array vectors led to 17 colonies containing bacteria with vector/left array. Left array protein band was captured using western blot assay. Conclusions and implications: ZFN might have off target on bacterial genome causing lethal double-strand DNA break due to lack of non-homologous end joining (NHEJ) mechanism. It is recommended to develop ZFNs against bacterial genes, engineered packaging host with NHEJ repair system is essential.
Can troxerutin pretreatment prevent testicular complications in prepubertal diabetic male rats?

Abstract Objective. The vast majority of type 1 diabetes leads to a higher prevalence of reproductive system’s impairments. Troxerutin has attracted much attention owing to its favorable properties, including antihyperglycemic, anti-inflammatory, and antiapoptotic effects. This investigation was proposed to evaluate whether pretreatment with troxerutin could prevent apoptosis-induced testicular disorders in prepubertal diabetic rats. Methods. Fifty prepubertal male Wistar rats were randomly allocated into five groups: control (C), troxerutin (TX), diabetic (D), diabetic+troxerutin (DTX), and diabetic+insulin (DI). Diabetes was induced by 55 mg/kg of streptozotocin applied intraperitoneally. In TX and DTX groups, 150 mg/kg troxerutin was administered by oral gavage. Diabetic rats in DI group received 2–4 U NPH insulin subcutaneously. Troxerutin and insulin treatments were begun immediately on the day of diabetes confirmation. After 30 days, the testicular lipid peroxidation and antioxidant activity, apoptosis process, and stereology as well as serum glucose and insulin levels were assessed. Results. The results showed that diabetes caused a significant increase in the blood glucose, the number of TUNEL positive cells and tubules, and the malondialdehyde level as well as a significant decrease in serum insulin level compared to controls. The stereological analysis also revealed various alterations in diabetic rats compared to controls. Troxerutin treatment improved these alterations compared to the diabetic group. Conclusion. Troxerutin-pretreatment may play an essential role in the management of the type-1 diabetes-induced testicular disorders by decreasing blood glucose and modulating apoptosis.
2L of Polyethylene Glycol as the Main Small Bowel Cleansing Regimen Component Prior to Video Capsule Endoscopy: Interim Analysis

Abstract Capsule Enteroscopy (CE) is a fundamentally new method in diagnostic endoscopy. However, there are several factors influencing the quality of this procedure, including impermeable fluids, food remains etc. The aim of the study was to assess one of the most popular currently used bowel preparation methods and evaluate possible effects of various factors. 136 CE examinations were analysed. Each patient was prepared using 2 litres of polyethylene glycol (PEG) one day prior to examination. There was a special form filled in for each patient, which included relevant parameters (anamnesis, CE data etc.). Of 136 CE cases, 84 (61.8%) were female patients and 52 (38.2%) were male. The small bowel (SB) transit time in 112 patients varied from 39 to 502 minutes, but in 24 cases the capsule did not reach caecum. The degree of bowel cleanliness was as follows: very good — 30 (22.1%) patients, satisfactory — 97 (71.3%), and poor — 9 (6.6%). A positive correlation was observed between the degree of SB cleanliness and the SB transit time (p = 0.015). A longer SB transits time was associated with poor SB cleanliness. The results obtained in this study showed that the quality of SB cleanliness is affected by SB transit time. A relatively large percentage of cases rated as satisfactory bowel cleanliness and comparatively small percentage of bowel cleanliness cases rated as “very good” were observed when 2 litres of PEG were used prior to CE, indicating an important issues in preparation of the bowel prior to CE.
Role of Stock Biomass and Temperature in Recruitment of Southern Gulf of St. Lawrence Atlantic Cod, Gadus morhua

LErr, P. F. , A. C. KoHr-er, e.No D. N. Frrzcennlo. 1975. Role of stock biomass and temperature inrecruitmentof southern Gulf of St. Lawrence Atlantic cod,Gadus morhua. J. Fish. Res, Board Can. 32: 1613-1627. A multivariate approach was used to elucidate the simultaneous effects of temperature and estimated parent stock biomass on the recruitment mechanism of Gulf of St. Lawrence cod. The second order effects of temperature and estimated stock biomass were key factors in determining egg abundance levels. In addition, egg abundance was closely related to the growth rate ofcod. The numbers of larvae increased with the interaction of temperature with egg abundance but decreased with the interaction of egg abundance and time. The most important step in the recruitment mechanism occurs during the juvenile stage, the degree of density dependence being reliant on total biomass of the adult cod stock. A system simulation was constructed amalgamating the equations of early life history of cod with the effects of exploitation on stock biomass. Regular 12-yr oscillations were demonstrated at low levels of catch, while the population became moie stable at higher fishing efforts in the absence ofenvironmental effects. The optimal fishing mortality for the Gulf of St. Lawrence cod was found to be F6.a, with a maximum sustainable yield of 42.000 metric tons.