Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic bases and phenotypic consequences of high-temperature adaptation in Escherichia coli

Author(s): Rodriguez Verdugo, Alejandra | Advisor(s): Gaut, Brandon S | Abstract: Connecting phenotype to genotype and fitness has been a major challenge when studying adaptation. Experimental evolution is a powerful method to facilitate the study of adaptation as an outcome and as a process. This dissertation used 114 clones of Escherichia coli that were evolved independently for 2000 generations under thermal stress (42.2oC). The goal of my dissertation was to link phenotypes and fitness with specific mutations and to identify the functional mechanisms leading to thermal adaptation.Chapter 1 focused on a subset of populations that became resistant to an antibiotic, rifampicin, during thermal stress adaptation. Rifampicin resistance was caused by three mutations at codon position 572 of the rpoB gene, which encodes the beta subunit of RNA polymerase (RNAP). I used samples from 200 generation intervals to assess the frequency trajectory of rifampicin resistance. I found that resistant mutations typically appeared, and were fixed, early in the evolution experiment. Finally, I confirmed that the three mutations conferred high advantage in glucose-limited medium at 42oC in the ancestral background.Chapter 2 investigated the same rpoB mutations in codon 572 to explore the molecular mechanisms underlying their fitness improvement at high temperature. I measured their growth curves and gene expression (mRNAseq) at 42oC, and compared them to the growth and gene expression of the ancestor at 37oC and 42oC. Two rpoB mutations restored the gene expression back to an ancestral state, while one mutation, exaggerated the expression changes of the ancestor at 42oC. Lastly, I compared the phenotypic characteristics of one single mutant, I572L, to those of two high-temperature adapted clones with this mutation. I concluded that the I572L mutation contributed to most of the expression changes while later mutations did not substantially changed gene expression.Chapter 3 explored the phenotypic consequences of high temperature adaptation in 114 clones. I measured the magnitude of fitness trade-offs across a thermal gradient. I identified two niche dynamics that I associated with two genetic pathways. Overall, my dissertation associates mutations to phenotypes in the context of thermal stress adaptation, and it highlights the difficulties of connecting genotype to phenotype, even if in a "simple" experimental system.
Genetic evaluation of drought tolerance in maize (Zea mays L.) inbred lines using tolerance indices

Genetic evaluation based on drought tolerant indices was conducted under moisture stress and well watered conditions using 98 maize inbreds along with four checks by following RBD with two replications. STI, GMP and MP are the most appropriate indices which determine drought tolerance and they showed high heritability coupled with high genetic advance over per cent mean. STI, GMP, MP, HARM, DI and K2 exhibited positive and significant association with grain yield under stress situation. Path coefficient analysis showed that positive and direct affect of MP, SSPI, K1 and RDI on grain yield in stress thus, direct selection based on these indices could be advisable to improve drought tolerance. Mahalanobi’s D2 analysis had found out the occurrence of wide range of diversity among the inbreds selected for study. Eight different clusters were formed, in which cluster I had 69 inbreds whereas, cluster VI and VII were singletons’, suggesting their uniqueness. Highest inter cluster distance was observed between cluster V and cluster VI where crossing can be recommended to develop drought tolerant heterotic hybrids. Mean of Stress tolerance index was high in cluster III it is comparable with tolerant check found in cluster V. Stress Tolerance Index was the major traits which contributed highest towards genetic diversity observed in the inbreds. Of the 98 inbreds considered for the evaluation, 30 inbreds showed minimum yield reduction (TOL) in stress condition. Among the 31 inbreds, MLB34, BLSB7-1, PDM 6572, PDM 6541and PDM 6529 were considered as tolerant based on Stress Susceptibility Index. Therefore, above study would serve the requirements for development of moisture stress tolerant hybrids by looking in to variability, character association, divergence and drought tolerant indices.
Identification and Susceptibility Testing of Non-Lactose Fermenting Gram-negative Bacilli in Urinary Tract Infection

Background: Urinary tract infections are one of the most common bacterial infections in humans both in community and hospital settings. The etiology of UTIs and the antimicrobial susceptibility of urinary pathogens have been changing over the years. Objectives: This work aimed to compare the accuracies of API 20E, Vitek1 system with GNI card with conventional reference biochemical tests for the identification of non-lactose fermenting Gram-negative bacilli in patients with urinary tract infection. Methodology: This study was conducted on 320 patients attending outpatient urology clinic. Physical, chemical, and microscopic examinations were done first to urine samples. Then, urine samples with pus cells <10 per high power field (HPF) or with bacterial cells or yeast were chosen for culture. These samples were 142 out 320 urine samples. These urine samples were isolated on nutrient, blood & MacConkey's agar media. Results: Standard bacteriological identification was done for all isolates (187 isolates) by colony morphology and microscopic examination. Only non-lactose fermenting Gram-negative bacilli (60 isolates) were further examined. Other growths were excluded. Motility test, biochemical reactions by conventional methods, API 20E, and vitek1 system with GNI card were done on non-lactose fermenting Gram-negative bacilli. Antibiotic susceptibility test by reference broth microdilution MIC procedure and Vitek1 system with GNI-108 card were done on non-lactose fermenting Gram-negative bacilli. One hundred thirty-five strains isolated from 94 hospitalized catheterized patients and fifty-two strains isolated from 48 outpatients sixty isolates (32.1%) were non-lactose fermenting Gram-negative bacilli. Out of them (thirty-one (16.5%) Pseudomonas aeruginosa, twenty (10.7%) Proteus mirabilis, six (3.2%) Proteus vulgaris, and three (1.6%) Providencia stuartii). After completion of supplemental tests, there was no difference between API 20E and vitek1 system in their ability to correctly identify Proteus mirabilis, Proteus vulgaris, and Providencia stuartii to the species level with there was difference between identifying isolates from Pseudomonas aeruginosa with vitek1 system. Conclusion: API 20E needs more time than vitek1 for identification of Proteus mirabilis, Proteus vulgaris, Providencia stuartii, and Pseudomonas aeruginosa, the most effective antibiotic against Pseudomonas aeruginosa isolates was ticarcillin/clavulant (77.4%), for Proteus mirabilis isolates were aztreonam and imipenem (each with 100%), for Proteus vulgaris isolates was imipenem (100%), and for Providencia stuartii isolates were amikacin, aztreonam, ciprofloxacin, imipenem, and TMP/SMX (100%).
Photoelectric and deep level study of metamorphic InAs/InGaAs quantum dots with GaAs confining barriers for photoluminescence enhancement

Metamorphic InAs/InGaAs quantum dots (QDs) have been proposed as active elements for optoelectronic light-emitting devices operating in the infrared range. However, advanced structure design to allow efficient and stable enhancement of quantum yield at room temperature are still needed. Here, we compare a metamorphic InAs/In0.15Ga0. 85As QD heterostructure with and without GaAs confining barriers, to investigate the effect of introducing GaAs barriers on the photo- and thermo-electrical properties. GaAs confining barriers allow to enhance the QD photoluminescence intensity at 1.3 µm, i.e. second telecommunication window, by more than two orders of magnitude at room temperature and at 80 K. We also discuss the effect of GaAs barriers on the carrier transport and on defect-related levels detected by means of photocurrent and deep level thermally stimulated current spectroscopies. GaAs confining barriers decrease the thermal escape rate of electrons confined in QD and wetting layer, thereby highly increasing the radiative recombination and also quenching the photocurrent. At low temperatures, the barriers also reduce the capture of electrons generated in InGaAs by the QD layer and, on the other hand, prevent the trapping of electrons outside the QD layer, decreasing carrier lifetimes. The deep levels identified as point and extended defects have been detected in the InGaAs layers. There are no new types of defects introduced in the structure by the addition of the barriers, but this causes a weakly increased density of traps near QDs. Our results show that InAs/InGaAs QDs with GaAs confining barriers can be efficient light emitters with only a slight increase of defects in the structure. Hence, such advanced design for metamorphic QDs can be of relevant interest for applications in energy-efficient QD lasers, optical amplifiers and single-photon emitters operating at 1.3–1.55 µm.
Calanus on the Bering Sea shelf: probable cause for population declines during warm years

Recent observations indicate that climate warming over the southeast Bering Sea shelf may negatively impact commercial and subsistence fish stocks by lowering abundance of large lipid-rich populations of Calanus. Warmer temperatures may impact Calanus by increasing metabolic rates and by altering food resources. We used published laboratory measurements on Calanus finmarchicus to develop a stage-specific individual base model to determine if Calanus populations on the southeastern Bering Sea shelf decline during warm years because of insufficient food concentrations, or because warmer winter temperatures elevate their metabolism during diapause, causing them to exhaust their lipid reserves before the onset of spring production. Results indicate that Calanus can reach its maximum size during both cold and warm years, but during warm winters, they will exhaust their lipid reserves during diapause by the end of December. During cold years Calanus can last into May of the following spring. Ice algae may provide a rich food source in March and April during cold years, before the spring phytoplankton bloom in May. Loss of Calanus on arctic and subarctic shelves may impact fish stocks which depend on Calanus for food.
Effect of different insecticides against fruit fly, Bactrocera cucurbitae Coquillett infesting sponge gourd

Field experiments on effect of different insecticides against fruit fly, Bactrocera cucurbitae Coquillett infesting sponge gourd was carried out during consecutive two years 2014 and 2015 at Agronomy Farm, Junagadh Agricultural University, Junagadh. The five different insecticides were evaluated against the fruit fly, B. cucurbitae infesting sponge gourd. The insecticides abamectin 0.0025 per cent and emamectin benzoate 0.002 per cent were found most effective and economic and were statistically at par with each other. The significantly minimum fruit infestation 19.35 per cent with 32.01 per cent yield increased and net return Rs. 22695/ha was recorded in the treatment of abamectin. While in emamectin benzoate 20.62 per cent fruit infestation with 29.10 per cent yield increased and Rs. 20625/ha net return was recorded. However, the treatment of dichlorovos 0.07 per cent (22.65% fruit infestation with 26.32% increased yield and Rs. 18660/ha net return) was proved next best insecticide.
TMJ Disc Displacement Angle Analysis in MRI: A New Proposal

Objective: To evaluate the co relation of clinical symptoms and MRI findings of TMJ in symptomatic Temporomandibular Dysfunction (TMD) patients. Material and Method: MRI TMJ scan of 25 patients were evaluated. The subjects had clinical evidence of reciprocal TMJ clicking or restricted mouth opening. This study determined the variability of temporomandibular joint (TMJ) disk position in antero-posterior aspect of the joint using magnetic resonance imaging (MRI). Disk position was evaluated on MRI by measuring the angle formed by a line through the middle of the condyle and tangential to the posterior-most aspect of the disk. Joint effusion was checked using T2 weighted image sequence. Thickness of superior and inferior head of lateral pterygoid muscle was measured. These MRI findings were then correlated statistically to clinical findings. Results: Out of 50 TMJ’s (25 patients); 40% had biconcave shape (no deformity), 16% cases showed lengthened disc, 12% cases showed a flattened disc, 12% cases showed thick posterior band. Varying degrees of disc displacement was associated with disc shape deformity. Increased thickness of Inferior head of lateral Pterygoid had statistically strong association with pain. Conclusion: A strong positive co relation was seen between the clinical and MRI findings in symptomatic TMD patients. Further using this, a new Disc Displacement angle measurement method and classification of disc shape was proposed for better disc evaluation.
Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes

Abstract Key innovations may allow lineages access to new resources and facilitate the invasion of new adaptive zones, potentially influencing diversification patterns. Many studies have focused on the impact of key innovations on speciation rates, but far less is known about how they influence phenotypic rates and patterns of ecomorphological diversification. We use the repeated evolution of pharyngognathy within acanthomorph fishes, a commonly cited key innovation, as a case study to explore the predictions of key innovation theory. Specifically, we investigate whether transitions to pharyngognathy led to shifts in the rate of phenotypic evolution, as well as shifts and/or expansion in the occupation of morphological and dietary space, using a dataset of 8 morphological traits measured across 3,853 species of Acanthomorpha. Analyzing the 6 evolutionarily independent pharyngognathous clades together, we found no evidence to support pharyngognathy as a key innovation; however, comparisons between individual pharyngognathous lineages and their sister clades did reveal some consistent patterns. In morphospace, most pharyngognathous clades cluster in areas that correspond to deeper-bodied morphologies relative to their sister clades, while occupying greater areas in dietary space that reflects a more diversified diet. Additionally, both Cichlidae and Labridae exhibited higher univariate rates of phenotypic evolution compared with their closest relatives. However, few of these results were exceptional relative to our null models. Our results suggest that transitions to pharyngognathy may only be advantageous when combined with additional ecological or intrinsic factors, illustrating the importance of accounting for lineage-specific effects when testing key innovation hypotheses. Moreover, the challenges we experienced formulating informative comparisons, despite the ideal evolutionary scenario of multiple independent evolutionary origins of pharyngognathous clades, illustrates the complexities involved in quantifying the impact of key innovations. Given the issues of lineage specific effects and rate heterogeneity at macroevolutionary scales we observed, we suggest a reassessment of the expected impacts of key innovations may be warranted.
Trace Mineral Leaching from Equine Compost

Mineral leaching from compost can be environmentally disruptive. Little information is available regarding trace mineral leaching from equine-sourced compost. The objective of this study was to quantify the mineral content and leaching potential of compost produced from feces of horses fed different amounts and forms (organic or inorganic) of trace minerals. Nine horses were fed three treatments in a 3 × 3 replicated Latin Square design. The dietary treatments were provided as a daily pellet: CON (pellet without added trace minerals), ING (added inorganic trace minerals), and ORG (added organic trace minerals). The added trace minerals were Co, Cu, Mn, and Zn. Feces were collected from each horse after a 16-day feeding period, combined with straw, composted, and then subjected to simulated rainfall to measure mineral mobility. Concentrations of Co, Cu, Mn, and Zn were greater in ING and ORG compared to CON compost (p < 0.05); additionally, ING had greater Zn than ORG compost (p < 0.05). More Cu leached from ING and ORG compared to CON (p < 0.05). The most Zn leached from ING, followed by ORG, and the least amount leached from CON compost (p < 0.05). Dietary trace mineral intake affected the trace mineral concentration in the compost and amount available to leach during rainfall events.
Fostering Enabling Perceptions of Management Controls During Post-Acquisition Integration

The purpose of this paper is to increase our understanding of how enabling perceptions of new management controls (MCs) can be fostered. We present a case study of an acquisition where the acquirer faces pressure to impose rigid controls on the acquired firm, who, in turn faces a massive restructuring and formalization of its controls. This study examines the response to new inflexible MCs implemented in a top down manner and the factors contributing to enabling perceptions. It shows that positive interpersonal relationships, and mutual trust between the acquirer and acquiree, facilitated enabling perceptions of the MCs. We show that managers actively fostered trust and communicated their intentions behind the design of controls. This helped employees rationalize the controls as tools to help them do their work tasks, i.e. enabling, rather than as a sign of mistrust, i.e. coercive. Positive interpersonal relationships reinforced by regular meetings were a way of providing employees assistance to deal with the problems they encountered through the rigidity of the new controls. This study contributes to the literature on enabling controls by proposing a processual framework based on trust-building activities that facilitates enabling perceptions among the employees. Thus, the study further develops our understanding of the relationship between enabling control and trust.
Atypical Presentation of Medullary Syndrome in a Young Woman

Wallenburg syndrome occurs due to damage to lateral segment of the medulla. Medial medullary syndrome occurs due to damage to upper portion of the medulla. I report a case of a 30 years old woman diagnosed with medullary syndrome [both medial & lateral features] in absence of CT scan findings sent to the department of Physiology for electrophysiological tests like nerve conduction studies, blink reflex, brainstem auditory evoked potential (BERA) & visual evoked potential (VEP). She had loss of sensations on the ipsilateral half of face (right), hemisensory loss on contralateral trunk & extremities, headache, contralateral hemiparesis (left), ipsilateral lingual paresis with atrophy, fibrillations with contralateral positive Babinski’s sign. The electrophysiological tests showed decrease in conduction velocity of right facial nerve, left tibial & peroneal nerves with decreased amplitude. The nerve conduction studies of median nerve (both motor & sensory) were normal. In blink reflex, latency of R2 ipsilateral & R2 contralateral of supraorbital nerves were increased on right side. There were increased latencies of waves II, III, IV & V of BERA & increased P100 latencies in VEP. The results of the electrophysiological tests of the patient showed that she had features of both medial & lateral medullary syndrome suggesting a lesion of both upper & middle medulla. The CT scan in this case was normal but conduction of MRI & CT guided angiography of posterior cerebral & vertebral arteries could have further localized the lesion causing this mixed symptomology. Case Report Sharma; JAMMR, 32(15): 6-11, 2020; Article no.JAMMR. 60717 7
Delayed nest predation: a possible tactic toward nests of open-nesting birds

Abstract. Predators use various tactics to find and depredate bird nests. This study examines a possible tactic of visually orientated predators termed “delayed nest-visit”. This consists in remembering the positions of incubating parents and subsequent easy depredation of eggs when the parents are away from their nests. Conditions for use of this tactic were experimentally simulated by installing artificial nests with quail eggs and plastic dummies of northern lapwings (Vanellus vanellus) at 11 actual breeding grounds with various habitat conditions in southern and eastern Bohemia, Czech Republic. Habitat, presence of the dummy, and their interaction significantly affected nest survival. While 17.2 % of the nests baited with the dummy were depredated, this occurred in only 6.9 % of the nests without the dummy. This depredation rate was affected by the visibility of the dummies in particular habitats. The results suggest that predators may remember the nest position to delay their first visit to a previously located bird nest from a remote place and may use this tactic to easily capture the clutches. The use of this tactic showed that at least some predator species are able to apply much more sophisticated approaches in search of birds' nests than previously assumed.
Confounding factors in exposure–response analyses and mitigation strategies for monoclonal antibodies in oncology

Dose selection and optimization is an important topic in drug development to maximize treatment benefits for all patients. While exposure–response (E‐R) analysis is a useful method to inform dose‐selection strategy, in oncology, special considerations for prognostic factors are needed due to their potential to confound the E‐R analysis for monoclonal antibodies. The current review focuses on 3 different approaches to mitigate the confounding effects for monoclonal antibodies in oncology: (i) Cox‐proportional hazards modelling and case‐matching; (ii) tumour growth inhibition–overall survival modelling; and (iii) multiple dose level study design. In the presence of confounding effects, studying multiple dose levels may be required to reveal the true E‐R relationship. However, it is impractical for pivotal trials in oncology drug development programmes. Therefore, the strengths and weaknesses of the other 2 approaches are considered, and the favourable utility of tumour growth inhibition–overall survival modelling to address confounding in E‐R analyses is described. In the broader scope of oncology drug development, this review discusses the downfall of the current emphasis on E‐R analyses using data from single dose level trials and proposes that development programmes be designed to study more dose levels in earlier trials.