Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early human germ cell development

During embryonic development, cells undertake a series of cell fate decisions to form a complete organism, epitomising a branching process. In some instances, these decisions are reversible, particularly during the onset of disease. Single cell transcriptomics provides a rich resource to explore the temporal progression of bifurcations in gene activity and are therefore useful for elucidating the mechanisms of cell fate decisions, provided that the cells can be suitably ordered over a developmental axis. Most methods for inferring this ordering have been developed for heterogeneous populations of cells collected at single time points, with few approaches specifically designed with structured data in mind, such as single cell time-series data. Recent advances based on Gaussian process latent variable models (GPLVMs) address this by allowing the incorporation of prior information, such as capture time, to yield more accurate ordering of cells. However, such approaches do not allow the ordering of cells over developmental processes with more than one branch. Here we develop a pseudotime approach that allows the ordering of cells over developmental trajectories with arbitrary numbers of branches, in the form of branch-recombinant Gaussian process latent variable models (B-RGPLVM). We use first demonstrate the advantage of our approach compared to existing pseudotime algorithms. Subsequently, we use B-RGPLVMs to infer cell ordering that occurs during early human development as primordial germ cells (PGCs), the precursors of sperm and egg, and somatic cells diverge in the developing embryo. Using our approach, we identify known master regulators of human PGC development, and predict roles for a variety of signalling pathways, as well as transcription factors and epigenetic modifiers. By concentrating on the earliest branched signalling events, we identified an antagonistic role for FGF receptor (FGFR) signalling pathway in the acquisition of competence for human PGC fate. We experimentally validate our predictions using pharmacological blocking of FGFR or its downstream effectors (MEK, PI3K and JAK), and demonstrate enhanced competency for PGC fate in vitro. Thus, B-RGPLVMs represent a powerful and flexible data-driven approach for dissecting the temporal dynamics of cell fate decisions, providing unique insights into the mechanisms of early embryogenesis. Software is available from: https://github.com/cap76/BranchingGPs
MCL-1 - Guardian of the Ovarian Reserve: Characterization of the Contribution of MCL-1 to Oocyte Survival

Oocyte quality and the maintenance of the ovarian reserve are essential factors in reproductive competence and fertility. The predominant portion of ovarian follicles are lost to natural death and the disruption of factors involved in conservation of the oocyte pool result in an untimely follicle exhaustion known as premature ovarian failure. Additionally, advancing maternal age is accompanied by accelerated follicle loss and the production of oocytes with poor developmental competence. Thus, identification of factors regulating oocyte quality and survival are essential in management and preservation of fertility. The anti-apoptotic Bcl-2 family member MCL-1 plays a pro-survival role in various cell types; however, its contribution to oocyte survival is unknown. In this thesis we characterized the phenotype caused by oocyte-specific Mcl-1-deficiency, and determined its role in the maintenance of the primordial follicle pool, growing oocyte survival and oocyte quality. Disruption of Mcl-1 resulted in a premature exhaustion of the ovarian reserve, characterized by early primordial follicle loss. The increasingly diminished surviving cohort of growing oocytes possessed elevated markers of autophagy and mitochondrial dysfunction. Ovulated Mcl-1 deficient oocytes displayed an increased susceptibility to cellular fragmentation with elevated iii activation of the apoptotic cascade. Concomitant deletion of the pro-apoptotic Bax rescued the primordial follicle phenotype and ovulated oocyte death, but did not impact mitochondrial dysfunction associated with Mcl-1-deficiency. Furthermore, we assessed the impact of the cytokine Kit ligand and metabolic supplementation, both associated with increased oocyte survival, on MCL-1 expression. We identified MCL-1 as a pro-survival target of these pathways in oocytes. Diminished Mcl-1-levels, both induced as well as physiologically driven, coincide with impaired mitochondrial output; resulting in starvationinduced autophagy and poor ovarian reserve. We classify MCL-1 as the essential survival factor required for maintenance of the primordial follicle pool, growing follicle survival and effective oocyte mitochondrial bioenergetics.
Functional evolution of R2R3 MYB transcription factors in the grasses

Transcription factors are emerging as key players in the origin of evolutionary novelties and as powerful tools to manipulating plant metabolism. The number of R2R3 Myb genes have amplified dramatically in the plants, where they are involved in the regulation of plant form and metabolic diversity. However, the function of most plant R2R3 Myb genes remains to be determined, primarily due to the lack of phenotypes of loss-of-function mutants. Here, we have investigated the evolutionary origins of R2R3 Myb genes and started to establish the functions of recently duplicated R2R3 Myb genes in maize through a gain-of-function approach. We have identified discrete evolutionary steps involved in the formation of plant specific R2R3 Myb genes from widely distribute R1R2R3 Myb genes. We have used the Black Mexican Sweet (BMS) maize cell culture system to investigate the consequences on the accumulation of metabolites of expressing the novel R2R3 MYB transcription factor ZmMYB-IF35. We demonstrate that, despite the high amino acid identity in the MYB domain with the P1 regulator of 3-deoxy-flavonoid biosynthesis, ZmMyb-IF35 does not induce the accumulation of flavonoids. However, similar to P1, ZmMyb-IF35 induces the accumulation of ferulic and chlorogenic acids, as well as several other compounds not found in the control BMS lines or in P1-expressing lines, suggesting a promising role of ZmMyb-IF35 for engineering the accumulation of various phenolic compounds. Together, our studies indicate that despite their recent common evolutionary origins, ZmMyb-IF35 and P1 have functionally diverged. These studies also suggest a possible correlation between phylogeny and function. Whether this is a general characteristic common to all regulatory genes remains to be determined. ii
Detection of Paratuberculosis in Migratory Gaddi Sheep of Himachal Pradesh using Pathological Techniques

The present study was planned to investigate the pathology of terminal ileum and associated lymph nodes in Gaddi sheep in Himachal Pradesh (HP) with particular emphasis on paratuberculosis. The tissue samples were collected from 39 sheep slaughtered for table purpose around Palampur and from Government slaughter house Shimla, Himachal Pradesh, during September, 2013 to March, 2014. The terminal ileum, along with ileo-caecal junction (ICJ) and associated lymph nodes were critically examined at gross and histopathology for lesions suggestive of paratuberculosis. The scrapping smear cytology of ileal mucosa and ileo-caecal lymph node (ICLN) was stained by Ziehl-Neelsenâ€™s (ZN) staining. Based on gross pathology, a total of 25(64.10%), 3(7.69%) and 1(2.56%) cases showed lesions suggestive of mild, moderate and severe paratuberculosis, respectively, with an overall 74.36% cases. ZN stained cytology demonstrated acid-fast bacilli (AFB) in 9 (23.08%) cases. On routine histopathological examination, the tissue samples were graded from 0 to IV and revealed only one (2.56%), 21 (53.84%), 13 (33.33%) and 3 (7.69%) Grade I, II, III and IV cases respectively, with an overall 97.43% cases. Only one histopathological Grade III case showed AFB (paucibacillary type) in ZN stained tissue sections from ileum and ileo-caecal lymph node (ICLN). Irrespective of the grade of paratuberculosis lesion the lymph nodes revealed mild to severe fibrosis in most of the cases suggesting replacement of granulomatous areas. In conclusion, histopathological examination was found to be the most effective method for detection of paratuberculosis in sheep and present study suggests alarming level of paratuberculosis among Gaddi sheep in HP.
First report of Verticillium dahliae Kleb. causing wilt symptoms in canola (Brassica napus L.) in North America

Abstract In Canada, Verticillium wilt of canola (Brassica napus L.), caused by Verticillium longisporum, was first confirmed in Manitoba in 2014. Verticillium dahliae, however, has not been reported to cause this disease. In 2016, a field survey in Alberta revealed canola plants with vascular wilt symptoms. Symptomatic plants were collected and infected stem tissue was cultured on agar medium, with one isolate designated A1-SS05 identified as a putative Verticillium spp. based on its colony characteristics. The colony was off-white in colour with a felt-like surface. On potato dextrose agar, the underside of the colony was dark only in the central area with radiating ridges. On Howell’s medium, only the test isolate exhibited polyphenol oxidase activity. The isolate formed conidiophores with 4–5 verticillate phialides. Mean conidial length was 5.96 µm (range of 4.65–6.64 µm) and mean width was 2.37 µm (range of 1.71–2.79 µm). The isolate also produced irregularly elongated chain-like microsclerotia of various sizes. Based on these criteria, isolate A1-SS05 was tentatively identified as V. dahliae. Sequencing of PCR products amplified with the primer sets ITS5/4 and VeruniF2/VeruniR3 revealed 99 and 100% identity, respectively, with V. dahliae sequences in GenBank, confirming the identity of this isolate. The isolate was pathogenic on the canola cultivar ‘Westar’, causing wilt symptoms, stunting, and leaf yellowing and senescence. Microscopic analysis of infected vascular tissues revealed irregular shaped microsclerotia, as were observed in pure culture. This is the first report of V. dahliae causing Verticillium wilt of canola in North America.
GREEN HERBAGE YIELD ASSESSMENTS OF MAIZE CULTIVARS THROUGH GGE BIPLOT ANALYSIS METHOD

The present study was conducted to assess green herbage yields of hybrid maize cultivars grown under different environments for two years. GGE biplot analysis method and regression coefficients were used to assess genotype x environment interaction and to identify the most stable cultivars for green herbage yield. Experiments were conducted in six different environments, green herbage yields in the environments varied between 6.0 t da-1 (E5) and 10.4 t da-1 (E1) and green herbage yield yields of the cultivars varied between 6.8 t da-1 (G14) and 10.9 t da-1 (G18). In GGE biplot analysis, the first two principle component (PC) axis explained about 82.45% of total variation. The genotypes with high PC1 and low PC2 values and regression coefficient of 1.0 were assessed as stable. The cultivar Safak (G18) with such values was identified as the most stable cultivar. The regression coefficient of 1.0 and the greatest green herbage yield proved the stability of that cultivar. The cultivars with higher PC1 and lower PC2 values [30B74 (G2), Seme Kukuruza 877 (G22), ADV 2898 (G24), Wayne (G17), and Safak (G18)] generally had higher green herbage yield than the general average. Safak (G18), 30B74 (G2), Seme Kukuruza 877 (G22), ADV 2898 (G24) and Wayne (G17) cultivars can be use green herbage yield production in south eastern Anatolia will allow the growers to have a profitable production.
Gene Induction by Nitric Oxide (NO) in Arabidopsis thaliana

Nitric Oxide (NO), which is important for mammalian defense response, plays also a central role in plants. To study the NO-dependent gene induction, NO-burst was simulated in cell culture as well as in plants (Arabidopsis thaliana) and the induced transcription was analysed by microarray analyses. About 10 percent of 330 tested stress genes were regulated by NO-treatment. Further biochemical and physiological studies were based on the microarray data. The induction of alternative oxidase (AOX1a) was shown to be an important factor against oxidative damage caused by NO treatment. Another interesting result was that NO correlated with the biosynthesis and signalling of the plant hormone jasmonic acid (JA). As in mammal, NO shows its influence on different cellular processes in plants.
A new species of Salamander (Caudata, Plethodontidae, Bolitoglossa ) from Serranía de los Yariguíes, Colombia

A new species of Bolitoglossa (Plethodontidae) is described from Andean cloud forests on the western slope of Serrania de los Yariguies in the Cordillera Oriental of Colombia. This new species is distinguished from all other species of the Bolitoglossa adspersa species group by differences in adult body size, morphometric proportions, and tooth counts. The validity of the new species is also supported by molecular analyses. This new species increases the number of salamander species in Colombia to 23 and highlights the Cordillera Oriental of Colombia, with 11 species, as the region with the highest diversity of Bolitoglossa in South America.
Anthropogenic emission inventories in China: a review

The development of reliable anthropogenic emission inventories is essential for both understanding the sources of air pollution and designing effective air-pollution-control measures in China. However, it is challenging to quantify emissions in China accurately, given the variety of contributing sources, the complexity of the technology mix and the lack of reliable measurements. Over the last two decades, tremendous efforts have been made to improve the accuracy of emission inventories, and significant improvements have been realized. More reliable statistics and survey-based data have been used to reduce the uncertainties in activity rates and technology distributions. Local emission factors and source profiles covering various sources have been measured and reported. Based on these local databases, improved emission inventory models have been developed for power plants, large industrial plants and the residential, transportation and agricultural sectors. In this paper, we review the progress that has been made in developing inventories of anthropogenic emissions in China. We first highlight the major updates that have been made to emission inventory models and the underlying data by source category. We then summarize the sector-based estimates of emissions of different species contained in current inventories. The progress that has been made in the development of model-ready emissions is also presented. Finally, we suggest future directions for further improving the accuracy of emission inventories in China.
Effects of subclinical Eimeria tenella infection on Pectoralis major muscle in broiler chickens

Abstract The aim of this study was to evaluate changes in the histological characteristics of the pectoralis major (PM) muscle in chickens as well as histological changes in the caecum after a low dose of Eimeria tenella (E. tenella). The chickens were inoculated orally with 5 × 102 E. tenella oocysts (Gr1) and 1 × 103 E. tenella oocysts (Gr2) at 16 days of age. Six chickens from each group were sacrificed for post mortem examination at 9 days post-infection (pi) and 16 days pi. Chicken growth was not affected by infection. On the 9th day of infection, caecal villus height was significantly greater in the non-infected control group. However, infected chickens from group Gr1 sacrificed seven days later had an even greater caecal villus height than those of the control (p =.001). Both infected groups had higher PM weights at 16 days pi than did the control group (p = .001). The fibre cross-sectional area was smaller in Gr2 at 9 days pi; however, this parameter was larger in these chickens at 16 days pi. The pH value of PM of group Gr2 was significantly higher than that of the control group or group Gr1 at 16 days pi (p = .020).
Studies on the molecular variability in Indian isolates of Papaya ringspot virus

Papaya ringspot virus (PRSV), Potyvirus is an important pathogen of papaya that causes severe losses in papaya production globally. The coat protein (CP) genes of four PRSV isolates originating from different locations in India, were cloned and sequenced. The band was observed at 840 bp in PRSV-FZD isolates of Uttar Pradesh. The isolates of PRSV have been characterized as papaya-infecting (PRSV-P). The PRSV-FZD sequence has made cluster with PRSV-Lucknow (AY458620). While sequences from Himanchal Pradesh (AY458617), Sikkim (DQ354072) clustered in another group with Jharkhand isolates (AY458619). Sequences from Karnataka (AY458618), Tamilnadu (DQ077175) and West Bengal (AY238885) have clustered in other group. The cluster analysis of the PRSV-FZD sequences and other Indian isolate has further done with PRSV sequences from different geographical regions. The results showed that PRSV-FZD had aligned in a cluster with other Indian sequences except sequences from Varanasi (AY238882), Maharashtra (AY238881), Madhya Pradesh (DQ650651) and Andhra Pradesh (AY903266) which clustered in separate groups. The sequences from Vietnam, China, Australia and Japan form a separate cluster. Brazil and USA sequences clustered in separate group along with the divergent Indian group.
Extracts from Thymus vulgaris and Origanum vulgare L. obtained by different separation processes: global yield and functional profile

The aim of this study was to quantify the amount of phenolic compounds and flavonoids in extracts from Thymus vulgaris and Origanum vulgare L. and to evaluate the antioxidant activity of these extracts. Extracts were obtained by employing three different techniques: low pressure solvent extraction, Soxhlet, and ultrasound methods. The effects of phenolic and flavonoid concentrations on the percentage of inhibition of free radical activity were also analyzed. The highest amounts of phenolic compounds were obtained with Soxhlet and Low Pressure Solvent Extraction (LPSE) for thyme and oregano respectively. The highest flavonoid levels were obtained by the Soxhlet extracts for both species. All extracts showed strong antioxidant activities.
Proximate composition and fatty acid profile in different tissues of juvenile Siganus guttatus fed with Enteromorpha prolifera

The proximate composition and fatty acid profile of five tissues (head, skin, bones, muscle and liver) of juvenile Siganus guttatus fed with Enteromorpha prolifera were investigated. The results indicated that: (1) The content of protein and fat among these five tissues showed a significant differences (P Lass Than 0.05). The muscle has the highest content of protein and the lowest content of fat. (2) The highest content of fatty acid in SFA is 16:0 in all five tissues, the highest content of fatty acid in MUFA is18:1n-9c (cis) in skin, bones, muscle and liver, while the highest content of PUFA is DHA in muscle. Muscle contained the highest value of DHA and EPA, the total content was more than 100 times in bones. Muscle tissue is rich in many important polyunsaturated fatty acids such as EPA, DPA, DHA, ARA and ALA, which has better nutritional quality and immune and health function.
Effect of Environmental Disturbances on Odonata Assemblages along a Tropical Polluted River

Abstract Odonata larvae have been intensively used as bioindicators for freshwater pollution as their community structure closely follow changes in the environment and habitat settings. In this study, 28 taxa of Odonata larvae were collected from three stations (upper, middle and lower) of a polluted river in Malaysia. The upper river basin receives effluents from an oil palm plantation. However, the middle station is presumably contaminated with anthropogenic wastes. The lower station is found to receive polluted discharges from aquaculture outlet. Several environmental parameters of water and sediment were continuously measured during the study. The water parameters showed no significant differences amongst the three stations. The species richness of Odonata was 22, 24 and 20 in the upper, middle and lower stations, respectively. The abundance of Odonata was significantly different among the studied sites. The tolerant damselfly, Pseudagrion sp. (41.22%), and facultative dragonflies, Onychothemis sp. (17.12%), were the most dominant taxa along the river stations. Onychothemis sp. and Paragomphus capricornis were equally important at the upper station [Important Species Index (ISI) 25.3 and 24.2%, respectively]. Pseudagrion sp. only scored an ISI value of 9.7%. Pseudagrion sp. , P. capricornis and Onychothemis sp. were dominant in the middle station (ISI: 41.2%, 25.9% and 10.9% respectively), and Pseudagrion sp. , Onychothemis sp. and Prodasineura sp. dominated the areas with dense growth of submerged aquatic weeds Hydrilla sp. in the lower station (ISI: 47.9, 24.5 and 13.8%, respectively). On the basis of the variations in larval abundance and ISI values, microhabitats differences partly in response to different types of pollutions entering the water structured the Odonata communities in this river basin.
Enhanced in vitro seed germination of economically important tree : Bixa orellana

Introduction Bixa orellana L. , commonly known as Annatto (also called as Chinese dye tree or the lipstick tree), belongs to the family Bixaceae and is native to tropical and subtropical regions of the world. The plant is mainly valued for its pigmented seeds that produce one of the dyes most frequently used worldwide (Poornima and Ambika, 2012). It is ranked the world's second most important natural colorant which is the major representative of the carotenoid family. The Annatto pigment is formed on the aril portions of the seeds of Bixa orellana plant. It is a mixture of eight colorants of carotenoid group, the predominant one is Bixin (>80 %). Along with bixin, it comprises of methylbixin, lutein, β-carotene, cryptoxanthin, zeaxanthin and norbixin (Venugopalan et al., 2011). It is also a richest source of terpene alcohol (Parimalan et al., 2010). Past few decades have seen an increased demand for natural colorant like annatto and other pigments due to the consumer ban on chemically synthesized azo dyes (Aher and Bairagi, 2012). Therefore, Annatto is being used in food products, cosmetic industries, pharmaceutical industries and also as fodder and fuel as it is safe, eco-friendly and non toxic natural dye. The dye has also been used in the treatment of many diseases like diabetics, measles, gonorrhea, diarrhea, kidney and skin diseases (Joseph and Siril, 2013). About 14,500 tons of annatto seeds are the estimated world consumption with an average cost of US$ 1100/mton of seeds (Vilar et al., 2014). The main commercial Abstract An efficient protocol was developed for in vitro seed germination of an