Miracle-dz/UniFAR-FTUs huggingface dataset:
Nutrient-dependent mTORC1 signaling in coral-algal symbiosis

To coordinate development and growth with nutrient availability, animals must sense nutrients and acquire food from the environment once energy is depleted. A notable exception are reef-building corals that form a stable symbiosis with intracellular photosynthetic dinoflagellates (family Symbiodiniaceae (LaJeunesse et al., 2018)). Symbionts reside in ‘symbiosomes’ and transfer key nutrients to support nutrition and growth of their coral host in nutrient-poor environments (Muscatine, 1990; Yellowlees et al., 2008). To date, it is unclear how symbiont-provided nutrients are sensed to adapt host physiology to this endosymbiotic life-style. Here we use the symbiosis model Exaiptasia pallida (hereafter Aiptasia) to address this. Aiptasia larvae, similar to their coral relatives, are naturally non-symbiotic and phagocytose symbionts anew each generation into their endodermal cells (Bucher et al., 2016; Grawunder et al., 2015; Hambleton et al., 2014). Using cell-specific transcriptomics, we find that symbiosis establishment results in downregulation of various catabolic pathways, including autophagy in host cells. This metabolic switch is likely triggered by the highly-conserved mTORC1 (mechanistic target of rapamycin complex 1) signaling cascade, shown to integrate lysosomal nutrient abundance with animal development (Perera and Zoncu, 2016). Specifically, symbiosomes are LAMP1-positive and recruit mTORC1 kinase. In symbiotic anemones, mTORC1 signaling is elevated when compared to non-symbiotic animals, resembling a feeding response. Moreover, symbiosis establishment enhances lipid content and cell proliferation in Aiptasia larvae. Challenging the prevailing belief that symbiosomes are early arrested phagosomes (Mohamed et al., 2016), we propose a model in which symbiosomes functionally resemble lysosomes as core nutrient sensing and signaling hubs that have co-opted the evolutionary ancient mTORC1 pathway to promote growth in endosymbiotic cnidarians.
Zelandoperla maungatuaensis sp. n. (Plecoptera: Gripopterygidae), a new flightless stonefly species from Otago, New Zealand

ABSTRACT A new wing-reduced species of the stonefly genus Zelandoperla Tillyard is described from Otago, New Zealand. Zelandoperla maungatuaensis sp. n. differs from a related species, Z. denticulata, primarily by lacking full wing development. We used morphological, geographical, and genetic evidence to assess the proposed status of Z. maungatuaensis sp. n. and Z. denticulata as separate monomorphic species, as opposed to conspecific members of a polymorphic species. High genetic divergence was found between distinctly allopatric populations, supporting the status of Z. maungatuaensis sp. n. as a distinct monomorphic species.
Optimal Installation of Overhead Lines (Tegusu) to Reduce Predation from Piscivorous Birds to Plecoglossus altivelis (Ayu) Taking into Account of Its Decaying Protection Effect

: This paper develops a simple mathematical model for determining an optimal installation timing of the overhead lines (Tegusu) to reduce predation from piscivorous birds, such as Phalacrocorax carbo (Kawau), to Plecoglossus altivelis (Ayu) taking into account of its decaying protection effect. Temporal dynamics of the total number and the individual body weight of P. altivelis are described with the system of ordinary differential equations for non-renewable population. Then, this paper formulates and numerically solves the governing equation of the optimal installation timing to simultaneously minimize the total predated P. altivelis and the cost to install and maintain the overhead lines. Extensive comparative statics of the optimal installation timing against model parameters is carried out to investigate its dependence on river environment and attitudes of decision makers.
Isolation and Identification of Cellulolytic Bacteria from Soil Sample and Their Antibiogram

This investigation was focused to isolate and identify the effective cellulolytic soil inhabiting bacteria from the soil of waste disposal site of Noakhali Science and Technology University (NSTU) campus and Maijdee, Noakhali with evaluating their cellulase production ability. Eight cellulolytic bacteria were isolated and identified as potentially effective strain from thirty isolates of twenty samples and their antibiogram was also performed. In this investigation, the maximum carboxymethylcellulose hydrolysis capacities (HC value), for all the isolates, ranged from 1.40 to 2.18 mm whereas maximum clear zone size around the colony ranged from 4.0 mm to 10.0 mm. It was the indication of the highest cellulase production ability of these eight species by degrading cellulose where two isolates sample 2 (10-3) and sample 15 (10-3) displayed the maximum zone of clearance around the colony. The results also revealed that soil of the investigated area can be used, in near future, to produce cellulase enzyme which will be useful for industrial purposes, plant growth promotion and research. Antibiotic sensitivity test was used in the work to determine the sensitivity and resistance pattern of the isolates. The result reported several isolates resistance to commercially used antibiotics. The main reason of this bacterial resistance is the indiscriminate use of the antibiotics. From the microscopic examination, morphological characteristics and various biochemical tests, the isolates were identified as Bacillus spp, Bacillus cereus, Bacillus megaterium, Clostridium spp, Staphylococcus aureus, Actinomycetes spp, Pseudomonas aeruginosa, Acinetobacter spp.
Sex-specific grazing dynamics of the recently described copepod, Lovenula raynerae, in an ephemeral pond in the Eastern Cape province of South Africa

This study investigated the temporal changes in the sex specific ingestion rates of the recently described calanoid copepod, Lovenula raynerae, which numerically and by biomass dominates the plankton community in ephemeral ponds in the Eastern Cape province of South Africa. Ingestion rates of the copepod were investigated on two occasions, one week after emergence and two weeks thereafter, employing the gut fluorescent technique. Results of the study indicate the absence of any diel patterns in feeding for both sexes on both sampling occasions (p > 0.05 in both cases). Moreover, there was no significant differences in gut pigment contents between adult male and females during either of the surveys (p > 0.05). Daily rations of the adult copepods during the two studies were equivalent to <2% (range 0.8 to 1.8%) body carbon per day suggesting that they are consuming alternative carbon sources to meet their daily carbon requirements. The main findings of this study suggest that L. raynerae can be considered as a generalist omnivore.
Toxic metals in agricultural soils near the industrial areas of Bangladesh: ecological and human health risk assessment

Abstract This study was conducted to assess the potential ecological and human health risk of toxic metals in agricultural soils near the industrial areas of Bangladesh. In this study, six toxic metals (chromium, nickel, copper, arsenic, cadmium, and lead) were assessed in 58 soil samples of five different sampling sites around the industrial areas of Jhenaidah and Kushtia districts in Bangladesh. Toxic metals were measured using inductively coupled plasma mass spectrometer. Potential ecological and human health risk were assessed through enrichment factor (EF), contamination factor (C f i), geoaccumulation index (I geo), pollution load index (PLI), toxic unit analysis, chronic daily intake through exposure pathway, hazard quotient, and hazard index. The mean concentrations of Cr, Ni, Cu, As, Cd, and Pb were found to be 5.78, 21.0, 31.8, 8.05, 1.20, and 19.2 mg/kg, respectively. Metals concentrations were found below the recommended value set by Dutch standard, Canadian guidelines, and Australian guidelines except Cd. Principal component analysis indicates that most of the metals in agricultural soils are coming from industrial sector. The mean values of EF, I geo, C f i, PLI, and toxic units were found safe level for all metals except Cd. In the view of potential ecological risk (PER), soils from all sampling sites indicated moderate to very high PER. Total target hazard quotients for all the studied metals in total sampling sites were <1 and cancer risk values were <10−6 indicating low noncarcinogenic and cancer risk for adult and children.
“Deciphering the amyloid foldome of TDP-43”

TDP-43 is an essential regulator of RNA splicing and metabolism and its aggregates play key roles in devastating diseases, including Amyotrophic Lateral Sclerosis (ALS)1, Frontotemporal Dementia (FTD) and Limbic-Predominant Age-Related TDP-43 Encephalopathy (LATE)2. Besides this pathological aggregation, TDP-43’s oligomerization also serves vital functions3, which adds urgency to determine pathological conformations of TDP-43. The recently published cryo-EM study by Cao, Eisenberg and coworkers now reveals amyloid structures of putative pathological aggregates from TDP-43’s C-terminal region4. Whereas the Cao et al.’s cryo-EM structures contain both the hydrophobic and Q/N-rich segments, the data were interpreted mainly through the lens of hydrophobic contacts. However, the Q/N-rich region can form amyloid on its own5,6 and therefore additional considerations of the Q/N-rich segment’s contributions will advance our understanding of TDP-43 aggregation.
Identification and phylogenetic analysis of herpes simplex virus-1 from clinical isolates in India

Human herpes simplex virus (HSV)-1 infection is acquired in childhood and persists throughout a person’s lifetime. Here, we present two cases from India; one showing symptoms of postpartum haemorrhage with disseminated intravascular coagulation, and the second one showing signs of acute encephalitis syndrome. The aetiological agent in both cases was identified as HSV-1 using the PCR method. The next-generation sequencing method retrieved ~97 % of the viral genome from the isolates of the clinical samples. The phylogenetic analysis of the retrieved genomes revealed that they belong to clade II of HSV-1. This study identifies a few sequence variations in the glycoprotein region of HSV-1 during two different clinical manifestations. There are a couple of papers that analyse variations in the glycoprotein region of clinical samples. Further, this study also highlights the importance of considering HSV-1 during differential diagnosis when analysing the nosocomial infection.
Intelligent Control for distillation columns

Nowadays, industrial processes are having to be rapidly developed to meet high standards regarding increases in the production rate and/or improving product quality. Fulfilling these requirements is having to work in tandem with the pressure to reduce energy consumption due to global environmental regulations. Consequently, most industrial processes critically rely on automatic control, which can provide efficient solutions to meet such challenges and prerequisites. For this thesis, an intelligent system design has been investigated for controlling the distillation process, which is characterised by highly nonlinear and dynamic behaviour. These features raise very challenging tasks for control systems designers. Fuzzy logic and artificial neural networks (ANNs) are the main methods used in this study to design different controllers, namely: PIPDand PID-like fuzzy controllers, ANN-based NARMAL2 in addition to a conventional PID controller for comparison purposes. Genetic algorithm (GA) and particle swarm optimisation (PSO) have also been utilised to tune fuzzy controllers by finding the best set of scaling factors. Finally, an intelligent controller is proposed, called ANFIS-based NARMA-L2, which uses ANFIS as an approximation approach for identifying the underlying systems in a NARMA-L2 configuration. The controllers are applied to control two compositions of a binary distillation column, which has been modelled and simulated in MATLAB® and on the Simulink® platform. Comparative analysis has been undertaken to investigate the controllers’ performance, which shows that PID-like FLC outperforms the other tested fuzzy control configurations, i.e. PIand PD-like. Moreover, PSO has been found to outperform GA in finding the best set of scaling factors and over a shorter time period. Subsequently, the performance of PID-like FLC has been compared with ANN-based NARMA-L2 and the proposed ANFIS-based NARMA-L2, by subjecting the controlled column to different test scenarios. Furthermore, the stability and robustness of the controllers have been assessed by subjecting the controlled column to inputs variance and disturbances situations. The proposed ANFIS-based NARMAL2 controller outperforms and demonstrates more tolerance of disturbances than the other controllers. Finally, the study has involved investigating the control of a multicomponent distillation column due to its significant enhancement in operational efficiency regarding energy saving and recent widespread implementation. That is, Kaibel’s distillation column with 4×4 configuration has been simulated also in MATLAB® and on the Simulink® platform with the proposed controller being implemented to control the temperatures of the column and the outcomes subsequently compared with conventional PID controllers. Again, the novel controller has proven its superiority regarding the disturbances tolerance as well as dealing with the high dynamics and nonlinear behaviour.
Beauty, memories and symbolic meaning: Swedish student teachers´ views of their favourite plant and animal

ABSTRACT In the twenty years since the first theory of ‘plant blindness’ was published much discussion has ensued concerning this phenomenon. More recent research, not only demonstrates that humans appear to favour animals over plants but also indicates a preference for mammals with forward-facing eyes. For this paper, we analysed answers to an online survey conducted with 202 student primary teachers in Sweden collected over a period of two years. We focus on two open-ended questions concerning favourite plant and animal choices and motivations for these choices. Our intention in this study was not to contrast animal vs. plant, but rather to further explore differential appreciation of plants and animals. Our findings suggest that there are large variations regarding relationships with plants and that affective connections with plant-life are translated through expressions of beauty, symbolic meaning, emotions (life-long) memories, colour, smell and size, and that similar characteristics seem to attract humans to animals. Our results – in line with arguments presented in recent studies – strongly suggest that in biological education and conservation contexts we should rely more intentionally on cultural and personal factors, utilise pre-existing experience-based human-plant bonds, and in so doing reinforce human recognition and appreciation of plants.
Microbial isolation from the gut of Channa punctata (Goroi fish) and study of their glycosidic activity

Microbial isolation from the gastro-intestinal tracts (only the midgut and hindgut) of Channa punctata have been performed to detect their importance in the digestion process of the experimental fish. Three types of microbes (bacteria and fungi) were separated from the GI tract of Channa punctata. Pure bacterial cultures were grown on Nutrient Agar (NA) media and were identified as Gram –ve cocci shaped bacteria through morphological test. While pure cultures of fungi were grown on Potato Dextrose Agar (PDA) media and were identified as Penicillium sp. and white sterile mycelia with no spore formation through morphological test. Intestinal isolates were checked for extra-cellular enzyme producing abilities by plate screening method. Amylolytic and cellulolytic microbes were found in the experimental fish’s gut. Cellulase activity was shown by all microbial isolates, while amylase activity was exhibited by the bacterial isolates and Penicillium sp. isolated from the GI tract of Channa punctata. Thus, from the experimented study, it can be concluded that, there would be a possibility of the digestive enzymes to be supplemented by the microbes of the experimental fish’s gut, which would be helpful in the preparation of diets, constituting or including the feeds that are non-conventional ones. Moreover, the microbes of the fish gut may help in the digestion process of the fish, and this study have isolated and identified the enzyme‐producing microbes.
Epidemiological survey of serum titers from adults against various Gram-negative bacterial V-antigens

The V-antigen, a virulence-associated protein, was first identified in Yersinia pestis more than half a century ago. Since then, other V-antigen homologs and orthologs have been discovered and are now considered vital molecules for the toxic effects mediated by the type III secretion system in infections caused by various pathogenic Gram-negative bacteria. After purifying recombinant V-antigen proteins including PcrV from Pseudomonas aeruginosa, LcrV from Yersinia, LssV from Photorhabdus luminescens, AcrV from Aeromonas salmonicida, and VcrV from Vibrio parahaemolyticus, we developed an enzyme-linked immunoabsorbent assay to measure titers against each V-antigen in the sera collected from 186 adult volunteers. Different titer-specific correlation levels were determined for the five V-antigens. The anti-LcrV and anti-AcrV titers shared the highest correlation with each other, with a correlation coefficient of 0.84. The next highest correlation coefficient was between anti-AcrV and anti-VcrV titers at 0.79, while the lowest correlation was found between anti-LcrV and anti-VcrV titers, which were still higher than 0.7 Sera from mice immunized with one of the five recombinant V-antigens displayed cross-antigenicity with some of the other four V-antigens, supporting the results from the human sera. Thus, the serum anti-V-antigen titer measurement system could potentially be used for epidemiological investigations on various pathogenic Gram-negative bacteria.
Gene Ontology and Expression Studies of Strigolactone Analogues on a Hepatocellular Carcinoma Cell Line

Human hepatocellular carcinoma (HCC) is the most common and recurrent type of primary adult liver cancer without any effective therapy. Plant-derived compounds acting as anticancer agents can induce apoptosis by targeting several signaling pathways. Strigolactone (SL) is a novel class of phytohormone, whose analogues have been reported to possess anticancer properties on a panel of human cancer cell lines through inducing cell cycle arrest, destabilizing microtubular integrity, reducing damaged in the DNA repair machinery, and inducing apoptosis. In our previous study, we reported that a novel SL analogue, TIT3, reduces HepG2 cell proliferation, inhibits cell migration, and induces apoptosis. To decipher the mechanisms of TIT3-induced anticancer activity in HepG2, we performed RNA sequencing and the differential expression of genes was analyzed using different tools. RNA-Seq data showed that the genes responsible for microtubule organization such as TUBB, BUB1B, TUBG2, TUBGCP6, TPX2, and MAP7 were significantly downregulated. Several epigenetic modulators such as UHRF1, HDAC7, and DNMT1 were also considerably downregulated, and this effect was associated with significant upregulation of various proapoptotic genes including CASP3, TNF-α, CASP7, and CDKN1A (p21). Likewise, damaged DNA repair genes such as RAD51, RAD52, and DDB2 were also significantly downregulated. This study indicates that TIT3-induced antiproliferative and proapoptotic activities on HCC cells could involve several signaling pathways. Our results suggest that TIT3 might be a promising drug to treat HCC.
Effect of Storage Containers and Lengths of Storage on the Germination, Moisture Content and Pest Infestation of Wheat Seed

A laboratory experiment was conducted at the Department of Agronomy, Hajee Mohammad Danesh Science and Technology University, Dianjpur-5200, Bangladesh to evaluate the storage containers and duration of seed storage on the germinability and health of wheat seeds. The experiment was carried out in two factors, viz. three storage containers naming i) sealed tin container, ii) plastic container, iii) gunny bag, and four storage periods of i) 15 days, ii) 30 days, iii) 45 days, and iv) 60 days. Completely randomized design (CRD) was used in this experiment with eight replications. The results revealed that the germination percentages (GP) of the seeds stored in the gunny bag decreased quickly from 66.1 to 32.8% due to contained with high moisture content in seed. But, slowly decreasing trends of GP from 80.4% to 69.2% was observed in the sealed tin container seeds with lesser moisture content than that of gunny bag and plastic container. The reduction of GP was so higher of 50.38% in the seeds contained in gunny bag than that of only 13.93% in the seeds contained sealed tin container. Wheat seeds stored in sealed tin container, plastic container and gunny bag significantly increased moisture content in ambient condition for 60 DAS. The moisture content of the seeds stored in gunny bag was found to rise remarkably more than other containers. This escalation of seed moisture content was closely related to the surrounding environmental conditions, like temperature and relative humidity where seeds were stored. The rate seed deterioration in gunny bag and plastic container paralleled the level of invasion by storage insect was found. During storage period, insect infected the seeds, and the insect bitten seeds were also found higher in gunny bag and plastic container, but lower in sealed container. Wheat seeds should be stored in air tight sealed container and drying should be done after some days of storage (45-60 DAS).
Evaluating the effects of rumen-protected glucose (RPG) on production, metabolism, and inflammation in transitioning dairy cows

The transition period is an energetically demanding time for the dairy cow. Successfully converting from a pregnant, non-lactating state to a non-pregnant, lactating state requires exquisite metabolic adaptations to ensure adequate glucose sparing for lactation onset. The inability to effectively partition nutrients towards lactation is associated with metabolic disorders. Dysfunctional glucose trafficking may not only predispose cows to maladapt to lactogenesis, but also limit milk synthesis and reproductive function during established lactation. Therefore, we hypothesized that glucose availability may limit milk yield (MY) during the transition period. Consequently, objectives were to determine the effects of feeding a rumen-bypass glucose product during the periparturient period on milk production, energetic metabolism, and inflammatory response in dairy cows.