Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome analysis of Arabidopsis to predict stress length-specific regulatory networks involved in drought response

Drought stress is one of the major environmental factors impairing crops productivity worldwide. Plants use various regulatory genes to reprogram genome activities to cope with such stresses. Among regulatory genes, transcription factors (TFs) function as terminal transducers and directly regulate the expression of wide spectrum of downstream genes. Multiplicity of the TF families and the complex interactions between TFs and cis-elements on the promoters of target genes as well as cross-talk between TFs in response to stress indicate the complexity of signaling networks involved in plant stress responses. This study aimed to use computational and statistical approaches to analyze a microarray dataset from Arabidopsis which covering different time periods of drought stress. After identifying and functional grouping of differentially expressed gens (DEGs), genes encoded TFs were determined and networked based on gene set enrichment analysis (GSE). Hierarchical regulatory network in each condition was assigned. After that, networks were used to conduct network topology analysis. Results indicated an obvious orientation in genome activity toward response to different cues; energy homeostasis and photosynthesis stability was occurred under drought stress. Also, 3787, 2931 and 5115 genes were differentially expressed under the early, moderate and prolonged drought stress, respectively, among them, 169, 140 and 261 TF were identified. Analysis of constructed regulatory networks of each drought condition revealed that plant recruits different but somewhat overlapping strategies to cope with stress in a long period of time. In each drought period, specific or common signaling pathways are activated using several numbers of transcription factors. It seems that among all identified TFs, ARR5, ARR6, ABF3, MYB29, MYB76 and SIGs genes are good candidate to manipulate plant stress tolerance.
MicroRNA regulation of macrophage activation

Macrophages are mononuclear phagocytic cells that have diverse roles within the body. Tissue specific macrophages, e.g. Kupffer cells, microglia and osteoclasts, have roles in tissue homeostasis, while circulating macrophages play an important role in the innate immune system. Macrophages detect the presence of pathogen associated molecular patterns (PAMPs) via a range of receptors known collectively as pathogen recognition receptors (PRRs). Detection of pathogens causes the macrophages to become ‘activated,’ during which the macrophages undergo extreme morphological and translational changes that enable the pathogen to be neutralised and other immune system components to be recruited. Macrophage activation must be carefully regulated and promptly resolved, as chronic inflammation is damaging to the host. MicroRNAs have emerged as one mechanism by which activation is regulated. MicroRNAs are small, non-coding pieces of RNA that function as a post-transcriptional regulatory mechanism. Their action is exerted through binding with a complementary region in the 3’ untranslated region (3’UTR) of the target mRNA. This binding, facilitated by the ribonuclear protein complex RISC, prevents successful translation of the mRNA into its protein product. MicroRNAs have been shown to function across species, throughout development and during the adult life-span. In the immune system, microRNAs are known to be required for correct formation of germinal centres and normal development of Band T-cells. MicroRNAs have also been shown to be differentially regulated during macrophage activation with different stimuli. In particular, miR-155, miR-146a and miR-21 are associated with macrophage activation by lipopolysaccharide (LPS). The objective of this work was to further understand the role of microRNAs during macrophage activation with LPS. Two approaches were adopted. Firstly, the regulation of individual microRNAs in LPS-activated bone marrow derived macrophages (BMDMs) was characterised by the use of illumina small RNA sequencing. Secondly, the requirement of the global microRNA population during macrophage biology was investigated through the use of DGCR8 and Dicer knockout systems. In keeping with the large number of changes reported in mRNA translation upon
Oxidative stress responses of Mytilus galloprovincialis to acute cold and heat during air exposure

We investigated the impacts of acute cold and heat exposure on mortality, oxidative stress, antioxidative and stress response, and apoptotic activation in gill tissue of Mytilus galloprovincialis. Our results showed that both cold (4 °C) and heat stress (35 °C) resulted in high mortality. Reactive oxygen species increased significantly after cold stress at 4 °C and heat stress at 30 °C (P < 0.01). In addition, both malondialdehyde content and antioxidative enzyme (SOD, CAT and GSH-Px) activities increased significantly after both cold and heat stress (P < 0.05). However, the transcripts of Hsp70 up-regulated only after heat stress. Western-blot analysis of gill extracts showed that the phosphorylation levels of p38-MAPK were enhanced only at the beginning of cold and heat stress, but elevated activation levels of caspase-3 were observed throughout a 24-h recovery period. Our results suggested that extreme cold and heat air exposure resulted in oxidative stress in the gill tissue of the mussels. The antioxidant enzymes are crucial under both cold and heat exposure, while Hsp70 is induced by heat stress. It seems that p38-MAPK plays a key role in the early response to both cold and heat stress and that apoptosis might be activated in the gill tissue of M. galloprovincialis.
Higher Intake of Milk-Replacer Pre-Weaning Enhances Post-Weaning Insulin-Like Growth Factor 1 Levels in Japanese Black Cattle

Alterations in early pre-natal nutrition of Japanese Black calves influence the glucose and lipid metabolism after weaning. However, the effects of early nutritional status on the endocrine system in later life stages in Japanese Black cattle are unknown. This study examined how post-weaning plasma levels of growth hormone (GH), insulin-like growth factor 1 (IGF-1), and blood insulin, which are hormones affecting growth and meat quality, and metabolites were affected by feeding 1800 g versus 500 g of milk replacer to Japanese Black cattle (5 per group) during nursing. Up to weaning (90 days post-birth), all calves received calf starter and hay ad libitum, and post-weaning, they received a concentrate feed and hay ad libitum. Plasma concentrations of GH and IGF-1 were greater at weaning in the high-milk-replacer group (P<0.1 and P<0.01, respectively), and elevated IGF-1 concentrations persisted until the study end (210 d) (P<0.05), suggesting that the levels were sustained independent of the influences of both GH and nutrient intake. Blood insulin and metabolites (plasma glucose, beta-hydroxybutyric acid, and non-esterified fatty acids) were not significantly different between the two groups. The results of this study suggest that feeding calves a high volume of milk replacer during nursing will increase IGF-1 secretion well beyond weaning.
Exact Tests of Zero Variance Component in Presence of Multiple Variance Components with Application to Longitudinal Microbiome Study

In the metagenomics studies, testing the association of microbiome composition and clinical conditions translates to testing the nullity of variance components. Computationally efficient score tests have been the major tools. But they can only apply to the null hypothesis with a single variance component and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to solve the problems of (1) testing the association of the overall microbiome composition in a longitudinal design and (2) detecting the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of human immunodeficiency virus (HIV) infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed lights on the impact of lung microbiome to HIV complexities. The method is implemented in the open source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.
Digestibility, growth, blood chemistry, and enzyme activity of juvenile Oreochromis niloticus fed isocaloric diets containing animal and plant byproducts

ABSTRACT In this work, we studied the digestibility, growth, blood chemistry, and enzyme activity of Nile tilapia (Oreochromis niloticus) juveniles (0.95±0.18 g) using different animal (fish silage meal, whey meal, bovine blood meal, and red crab meal) and plant (extruded bean, extruded chickpea meal, coconut paste, Jatropha curcas meal, and chickpea meal) dietary byproducts. Nine isocaloric diets (321.92±9.10 kcal g−1) were evaluated for 60 days. The highest digestibility of crude protein values for animal and plant sources were obtained for [. ]
Preliminary Evaluation of Pre- and Post-Prandial 3α- Hydroxy Bile Acids in the Green Iguana, Iguana iguana

ABSTRACT Pre- and post-prandial plasma 3α-hydroxy bile acids and other biochemical reference intervals were established for a group of 11 healthy male green iguanas, Iguana iguana. All animals were fasted for 48 hr and then fed a herbivorous, commercially available critical care diet containing 606 +/− 52.6 mg of fat per kg body weight to stimulate bile release. Pre-prandial bile acid concentrations (7.5 ± 7.8 μmol/L) significantly increased at 3 and 7.5 hr post-prandially to 33.3 ± 22.0 μmol/L and 32.5 ± 8.4 μmol/L, respectively. Liver histopathology and general necropsy findings were unremarkable. This study demonstrated a significant increase in post-prandial plasma 3α-hydroxy bile acid concentration in healthy green iguanas. This study suggests that fasting status should be considered when evaluating bile acid concentrations.
Detection of luxS Gene in Serratia marcescens and rpoS Gene in Enterobacter cloacae Isolates Using PCR Reaction

luxS and rpoS genes were involved in the regulation of some biological processes, which interfere with virulence of Serratia marcescens and Enterobacter cloacae bacterial species sequentially. luxS have an important activity in Quorum Sensing (QS) processes, but rpoS interfere with tolerance and resistance processes toward stress conditions correlating with its virulence. The study aimed to detect rpoS presence in E. cloacae and luxS gene presence in S. marcescens separately isolated from 16 leukaemia patients (4 of S. marcescens and 12 of E. cloacae), who characterised with bacteraemia by using primers designed for this purpose by using PCR technique. The results showed that all of the bacterial isolates of S. marcescens contain luxS gene, while no one of E. cloacae isolates show positive results for rpoS gene. The study concluded that S. marcescens has high virulence as a result of luxS presence, which controls Quorum sensing and prodigiosin formation and affecting host immunity. Moreover, the negative results of rpoS gene can be explained according to two possibilities: the gene can be found in the isolates with a copy differ from the registered sequences of the rpoS gene, or the gene did not present in those isolates with presence of alternatives offset its activities
Museum Specimens Bias Measures of Snake Diet: A Case Study Using the Ambush-Foraging Puff Adder (Bitis arietans)

Abstract: Examination of the gastrointestinal contents of museum specimens is routinely used as a method for assessing diet in a wide variety of reptiles. However, this method might be biased toward detecting prey items that are less digestible and larger in size because these food items are digested more slowly. In this study, we used fixed videography on free-ranging Puff Adders (Bitis arietans) as a comparative, data-collecting technique to assess the accuracy of the traditional method of examination of the gastrointestinal tracts of museum specimens as a measure of diet. The data-collecting method affected our measures of diet: Analyses relying on museum specimens showed a much narrower diet breadth compared to fixed videography, and measures of mean relative prey mass were more than three times larger using museum specimens compared to fixed videography. Our findings demonstrate that data collected through fixed videography and examination of museum specimens provide different perspectives of a snake's diet because of the biases associated with museum specimens. As a result, the use of museum specimens to assess diet should be interpreted cautiously and with knowledge of these biases, as the technique might only reveal certain aspects of a species trophic ecology. In particular, we suggest that the routine use of methods such as examination of museum specimens and palpation of live snakes might have led to a biased interpretation of the feeding ecology of ambush-foraging snakes.
Exploring the potential of providing and feeding pikeperch larvae (Sander lucioperca L.) with euryhaline copepod nauplii: A zoo technical trial

ABSTRACT Egg hatching and nauplii success from three euryhaline calanoid copepod species at low salinities suggest a promising alternative initial live feed for pikeperch (Sander lucioperca L.) to the conventional live feed. Acartia bifilosa and Eurytemora affinis are viable candidates with egg hatching down to zero salinity, and Acartia tonsa nauplii survive up to 2 h at zero salinity after transfer from low-salinity seawater. When offered A. tonsa and Artemia, pikeperch larvae equally consumed both prey types. We suggest that euryhaline copepods can be a supplement to or even a substitute for the normal live feed currently used as larval feed for pikeperch.
Investigation of host factors involved in Legionella pneumophila virulence

i Declaration . iii Preface . iv List of publications arising from this thesis . v Acknowledgements . vi Abbreviations . ix Table of contents . xii List of tables and figures . xvii Chapter 1: Literature review . 1 1.1 Historical Perspective . 1 1.2 Characteristics of Legionella bacteria . 1 1.3 Legionellosis – Legionnaire’s disease and Pontiac fever . 2 1.3.1 Clinical manifestation . 2 1.3.2 Diagnosis strategies . 3 1.3. 3 Treatment . 4 1.4 Legionella – an opportunistic human pathogen . 5 1.4. 1 Ecology . 5 1.4. 2 Transmission . 6 1.4. 3 Life cycle . 7 1.5 L. pneumophila infection strategy . 8 1.5. 1 Entry into macrophages . 8 1.5. 2 Formation of the Legionella-containing vacuole . 10 1.5. 3 Exit from macrophages . 11 1.6 Protein secretion systems of L. pneumophila . 13 1.6. 1 The Lsp Type II secretion system and its substrates . 13 1.6. 2 The Lss and Tat secretion systems . 14 1.6. 3 Type IV secretion system . 15 1.6. 3.1 Lvh Type IVA secretion system . 15 1.6. 3.2 The Dot/Icm TypeIVB secretion machinery . 15 1.6. 4 Substrates of the Dot/Icm system . 17 1.7 Modulation of host cell processes by Dot/Icm substrates . 18
Histopathological classification and immunohistochemical characterization of canine mammary tumours

The present study was carried out to investigate breed wise and age wise prevalence of canine mammary tumours (CMTs) along with histopathological and immunohistochemical characterization. A total of 97 CMTs samples were collected from different parts of Gujarat, India over period of three years (April 2014-March 2017). The mean age of the dogs, involvement of breeds and mammary glands were recorded. The mean±SD age of all affected dogs was 7.5±2.8 years. Among 12 breeds affected, most cases (n=77) of CMTs were recorded in four breeds viz., Pomeranian, Mongrel, Germen Shepard and Labrador. Caudal abdominal and inguinal mammary glands were frequently showed neoplastic growth. Among histological characterization of 97 CMTs, 16(16.49%) were non neoplastic proliferative/dysplastic lesions, 11 (11.34%) were benign neoplasms and 70 (72.16%) were malignant tumours. Out of 70 malignant neoplasms, epithelial neoplasms, special type epithelial neoplasms, mesenchymal neoplasms and carcinosarcomas were 53(54.64%), 6(6.19%), 8(8.25%), and 3(3.09%), respectively. Further, mixed carcinoma, tubulopapillary carcinoma, solid carcinoma, carcinoma and malignant myoepithelioma, tubular carcinoma and ductal carcinoma were frequently noted. Immunohistochemistry was found to be a powerful tool to classify the CMTs. In the present study, smooth muscle actin (SMA) helped in diagnosing complex adenoma, complex carcinoma, malignant myoepithelioma and fibrosarcoma. In complex adenoma, complex carcinoma and malignant myoepithelioma, myoepithelial cells showed strong SMA immunoreactivity, although stromal myofibroblasts and vascular smooth muscle cells also immunostained.
Conservation of wild silkworm genetic resources through cryopreservation: Standardization of sperm processing

Conservation of the invaluable sericigenous genetic resources is of prime importance with respect to their utilization and improvement for wider exploitation. Conservation of wild silkworms and its applicability in hybridization have limitations due to incompatibility, less amenability, change of behaviour under ex situ conditions, non-synchronization of moth eclosion and difficulties in mating between variables. In view of this, the newer technologies such as cryopreservation and artificial insemination are offering better strategies for preservation of biologically active samples like semen at sub-zero temperature (-196º C) conditions for longer duration. In this context, under standardization of sperms preservation from wild silkworms, two methods of semen collection were scrutinized for obtaining active and viable sperm for cryopreservation and further artificial insemination. Semen collection from the seminal vesicle of freshly emerged male moth and the other from the bursa copulatrix (BC) and spermatheca of the female moth after mating. The sperms in the semen collected from seminal vesicle are in the form of bundles known as eupyrene sperm bundles and apyrene sperms. The morphology and behaviour of these sperm bundles were recorded through microscopic examination. To study the density and motility behaviour of the sperms, sperm bundles were treated with proteolytic enzyme (~2-3µg/ml) to digest the membrane and release the sperms. The density and motility behaviour of sperms in the semen recovered from the BC and spermatheca of female moth after mating were higher compared to those released after digestion of sperm bundles from seminal vesicle of the male moth.
OCCURRENCE AND IDENTIFICATION OF CEREAL CYST NEMATODE, HETERODERA FILIPJEVI (NEMATA: HETERODERIDAE), IN BOLU PROVINCE OF TURKEY

Cereal cyst nematodes, Heterodera filipjevi, parasitize the roots of wheat and cause significant yield losses around the world. Cereal cyst nematodes are one of the most important and endemic problems in wheat-growing areas especially where rainfall is limited and monoculture crop production practices exist. In Turkey, cereal cyst nematodes are considered among the most damaging pests in wheat. Identifying cyst nematode species and determining their prevalence and distribution in Turkey are important for predicting potential spread in the future. This survey aimed to identify cyst nematode species and to assess their prevalence in cereal growing areas of Bolu province in Turkey. Cereal cyst nematode cysts were found in 83% of the surveyed fields. Prevalence of cysts was greater in cereal-growing areas in the provincial center and in the Gerede district. Morphological features of second-stage juveniles and cysts were examined, and DNA was extracted from second-stage juveniles and the species-specific Sequence Characterized Amplified Region (SCAR) primers were used for molecular identification. Based on both morphological and molecular methods, all samples were identified as H. filipjevi. This study was the first comprehensive investigation of H. filipjevi prevalence in cereal fields in Bolu. This information is of value to alert personnel of wheat breeding programs to develop local resistant varieties to target H. filipjevi.
Modeling the Efficiency of Sampling and Trapping Varroa destructor in the Drone Brood of Honey bees (Apis mellifera)

A computer model simulating varroa mite (Varroa destructor— previously known as Varroa jacobsoni) infestation in colonies of honey bees (Apis mellifera) confirmed that, due to the preference of mites to invade drone (male) honey bee brood to reproduce, a very high proportion of the mite reproduction could occur in a relatively small amount of drone brood. Several regimes of sampling or removing drone bee pupae to estimate or remove numbers of varroa mites were simulated to compare their effectiveness. The model indicated that regular sampling of at least 100 drone pupae could provide the beekeeper with a useful warning of when numbers of varroa were approaching damaging levels. An infestation level of 15% of drone pupae would be a conservative threshold to indicate treatment was imminently required. The model indicated that significant reduction of mite numbers could be achieved either by very regular uncapping and removal of most of the natural drone pupae, or by trapping mites in artificially high numbers of drone pupae. The numbers of drone pupae required to significantly delay the mite build-up could be reduced considerably by trapping at a time when the bee colony was otherwise broodless. However, the varroa numbers were not controlled sufficiently by drone brood removal alone in any of the regimes tested.
Complete mitochondrial genome sequence of Hemiculter bleekeri

Abstract In our research, the complete mitochondrial DNA (mtDNA) of Hemiculter bleekeri was obtained from the dorsal myotome of the fish. The total length of the mitochondrial genome is 16,617 bp and deposited in GenBank with accession number KU198332. The gene arrangement was similar to other bony fishes, which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region. The mtDNA may provide some important genetic background information of this valuable fish. The G contents was relatively low in the total mtDNA with the GCskewthinsp;= −0.22. The negative GC-skew ranging from −0.51(ATP8) to −0.19(CO1), and the more positive AT-skew varying from −0.26(ATP8) to −0.03(CO1). The phylogenetic analysis demonstrated that H. Bleekeri was clustered together with Hemiculter leucisculus, which could be a sister species.