Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence

Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.

Increased privatization of a public resource leads to spread of cooperation in a microbial population

The phenomenon of cooperation is prevalent at all levels of life. In one such manifestation of cooperation in microbial communities, some cells produce costly extracellular resources that are freely available to others. These resources are referred to as public goods. Saccharomyces cerevisiae secretes invertase (public good) in the periplasm to hydrolyze sucrose into glucose and fructose, which are then imported by the cells. After hydrolysis of sucrose, a cooperator retains only 1% of the monosaccharides, while 99% of the monosaccharides diffuse into the environment and can be utilized by any cell. The non-producers of invertase (cheaters) exploit the invertase-producing cells (cooperators) by utilizing the monosaccharides and not paying the metabolic cost of producing the invertase. In this work, we investigate the evolutionary dynamics of this cheater-cooperator system. In a co-culture, if cheaters are selected for their higher fitness, the population will collapse. On the other hand, for cooperators to survive in the population, a strategy to increase fitness would likely be required. To understand the adaptation of cooperators in sucrose, we performed a coevolution experiment in sucrose. Our results show that cooperators increase in fitness as the experiment progresses. This phenomenon was not observed in environments which involved a non-public good system. Genome sequencing reveals duplication of several HXT transporters in the evolved cooperators. Based on these results, we hypothesize that increased privatization of the monosaccharides is the most likely explanation of spread of cooperators in the population.IMPORTANCEHow is cooperation, as a trait, maintained in a population? In order to answer this question, we perform a coevolution experiment between two strains of yeast-one which produces a public good to release glucose and fructose in the media, thus generating a public resource, and the other which does not produce public resource and merely benefits from the presence of the cooperator strain. What is the outcome of this coevolution experiment? We demonstrate that after ~200 generations of coevolution, cooperators increase in frequency in the co-culture. Remarkably, in all parallel lines of our experiment, this is obtained via duplication of regions which likely allow greater privatization of glucose and fructose. Thus, increased privatization, which is intuitively thought to be a strategy against cooperation, enables spread of cooperation.

Ecological disruptive selection acting on quantitative loci can drive sympatric speciation

The process of speciation generates biodiversity. According to the null model of speciation, barriers between populations arise in allopatry, where, prior to biology, geography imposes barriers to gene flow. On the other hand, sympatric speciation requires that the process of speciation happen in the absence of a geographical barrier, where the members of the population have no spatial, temporal barriers. Several attempts have been made to theoretically identify the conditions in which speciation can occur in sympatry. However, these efforts suffer from several limitations. We propose a model for sympatric speciation based on adaptation for resource utilization. We use a genetics-based model to investigate the relative roles of prezygotic and postzygotic barriers, from the context of ecological disruptive selection, sexual selection, and genetic architecture, in causing and maintaining sympatric speciation. Our results show that sexual selection that acts on secondary sexual traits does not play any role in the process of speciation in sympatry and that assortative mating based on an ecologically relevant trait forces the population to show an adaptive response. We also demonstrate that understanding the genetic architecture of the trait under ecological selection is very important and that it is not required for the strength of ecological disruptive selection to be very high in order for speciation to occur in sympatry. Our results provide an insight into the kind of scenarios in which sympatric speciation can be demonstrated in the lab.

Rapid evolution of pre-zygotic reproductive barriers in allopatric populations

IMPORTANCE

A population diversifies into two or more species-such a process is known as speciation. In sexually reproducing microorganisms, which barriers arise first-pre-mating or post-mating? In this work, we quantify the relative strengths of these barriers and demonstrate that pre-mating barriers arise first in allopatrically evolving populations of yeast, Saccharomyces cerevisiae. These defects arise because of the altered kinetics of mating of the participating groups. Thus, our work provides an understanding of how adaptive changes can lead to diversification among microbial populations.

Significant enhancement in the cold emission characteristics of chemically synthesized super-hydrophobic zinc oxide rods by nickel doping

The current article presents a huge enhancement in the field emission characteristics of zinc oxide (ZnO) micro/nanorods by nickel doping. The synthesis of pure and nickel-doped zinc oxide (ZnO) micro/nanorods was done by a simple low-temperature chemical method. Both the as-prepared pure and doped samples were analyzed by X-ray diffraction and electron microscopy to confirm the proper phase formation and the developed microstructure. UV-vis transmittance spectra helped in determining the band gap of the samples. Fourier-Transform Infrared Spectroscopy (FTIR) spectra showed the different bonds present in the sample, whereas X-ray Photoelectron Spectroscopy (XPS) confirmed the presence of nickel in the doped sample. Photoluminescence (PL) spectra showed that after doping, the band-to-band transition was affected, whereas defect-induced transition had increased significantly. After the nickel doping, contact angle measurement revealed a significant decrease in the sample's surface energy, leading to a remarkably high water contact angle (within the superhydrophobic region). Simulation through ANSYS suggested that the doped sample has the potential to function as an efficient cold emitter, which was also verified experimentally. The cold emission characteristics of the doped sample showed a significant improvement, with the turn-on field (corresponding to J = 1 μA cm-2) reduced from 5.34 to 2.84 V μm-1. The enhancement factor for the doped sample reached 3426, approximately 1.5 times higher compared to pure ZnO. Efforts have been made to explain the results, given the favorable band bending as well as the increased number of effective emission sites.

Establishing proof of concept for utility of Trueprep®-extracted DNA in line-probe assay testing

BACKGROUND AND OBJECTIVES: With an increased demand for rapid, diagnostic tools for TB and drug resistance detection, Truenat® MTB-RIF assay has proven to be a rapid point of care molecular test. The present study aimed to establish a proof of concept of using Trueprep-extracted DNA for line-probe assay (LPA) testing.METHODS: A total of 150 sputum samples (MTB-positive at Truenat sites) were divided into two aliquots. One aliquot was used for DNA extraction using the Trueprep device and MTB testing. The second aliquot of the sample was subjected to GenoLyse® DNA extraction. DNA from both the Trueprep and GenoLyse methods was subjected to first-line (FL) and second-line (SL) LPA testing.RESULTS: Of 139 Trueprep-extracted DNA, respectively 135 (97%) and 105 (75%) had interpretable results by FL and SL-LPA testing. Of 128 GenoLyse-extracted DNA, all 128 (100%) had interpretable FL-LPA results and 114 (89%) had interpretable SL-LPA results.CONCLUSION: The results obtained in this study indicate that Trueprep-extracted DNA can be used in obtaining valid LPA results. However, the study needs to be conducted on a larger sample size before our recommendations can be used for policy-making decisions.

PHEOCHROMOCYTOMA, THE GREAT MASQUERADER, PRESENTING AS REVERSIBLE CARDIOMYOPATHY: PRIMUM NON NOCERE

Background

Pheochromocytoma, the great masquerader, can have a varied spectrum of clinical manifestations. It can often cause a diagnostic challenge despite the availability of modern investigation modalities.

Case

We present the case of a 38-year-old male who presented with uncontrolled hypertension for the past 10 years and heart failure for one year. The diagnosis of pheochromocytoma was missed in the initial setting, leading to a biopsy of the retroperitoneal mass. Fortunately, the patient survived the procedure. Subsequently, with the involvement of a multi-disciplinary team, he was optimized for surgery under strict cardiac monitoring. After the complete excision of the tumour, he showed significant improvement not only in his clinical symptoms but also in his cardiac status.

Conclusions

This case emphasizes the age-old medical phrase of 'Primum non nocere or first, do no harm'. Any invasive procedure in a pheochromocytoma can lead to a massive release of catecholamines causing a hypertensive crisis, pulmonary oedema, and even cardiac arrest. Any young patient presenting with hypertension or heart failure should be investigated for secondary causes. Cardiomyopathy due to pheochromocytoma is because of catecholamine overload and usually reverses or improves after curative surgery.

Exploring the Influence of pH on the Dynamics of Acetone-Butanol-Ethanol Fermentation

Clostridium acetobutylicum is an anaerobic bacterium that is extensively studied for its ability to produce butanol. Over the past two decades, various genetic and metabolic engineering approaches have been used to investigate the physiology and regulation system of the biphasic metabolic pathway in this organism. However, there has been a relatively limited amount of research focused on the fermentation dynamics of C. acetobutylicum. In this study, we developed a pH-based phenomenological model to predict the fermentative production of butanol from glucose using C. acetobutylicum in a batch system. The model describes the relationship between the dynamics of growth and the production of desired metabolites and the extracellular pH of the media. Our model was found to be successful in predicting the fermentation dynamics of C. acetobutylicum, and the simulations were validated using experimental fermentation data. Furthermore, the proposed model has the potential to be extended to represent the dynamics of butanol production in other fermentation systems, such as fed-batch or continuous fermentation using single and multi-sugars.

Determination of the Mating Efficiency of Haploids in Saccharomyces cerevisiae

Saccharomyces cerevisiae is a widely used model organism in genetics, evolution, and molecular biology. In recent years, it has also become a popular model organism to study problems related to speciation. The life cycle of yeast involves both asexual and sexual reproductive phases. The ease of performing evolution experiments and the short generation time of the organism allow for the study of the evolution of reproductive barriers. The efficiency with which the two mating types (a and α) mate to form the a/α diploid is referred to as the mating efficiency. Any decrease in the mating efficiency between haploids indicates a pre-zygotic barrier. Thus, to quantify the extent of reproductive isolation between two haploids, a robust method to quantify the mating efficiency is required. To this end, a simple and highly reproducible protocol is presented here. The protocol involves four main steps, which include patching the haploids on a YPD plate, mixing the haploids in equal numbers, diluting and plating for single colonies, and finally, calculating the efficiency based on the number of colonies on a drop-out plate. Auxotrophic markers are employed to clearly make the distinction between haploids and diploids.

Public good-driven release of heterogeneous resources leads to genotypic diversification of an isogenic yeast population

Understanding the basis of biological diversity remains a central problem in evolutionary biology. Using microbial systems, adaptive diversification has been studied in (a) spatially heterogeneous environments, (b) temporally segregated resources, and (c) resource specialization in a homogeneous environment. However, it is not well understood how adaptive diversification can take place in a homogeneous environment containing a single resource. Starting from an isogenic population of yeast Saccharomyces cerevisiae, we report rapid adaptive diversification, when propagated in an environment containing melibiose as the carbon source. The diversification is driven due to a public good enzyme α-galactosidase, which hydrolyzes melibiose into glucose and galactose. The diversification is driven by mutations at a single locus, in the GAL3 gene in the S. cerevisiae GAL/MEL regulon. We show that metabolic co-operation involving public resources could be an important mode of generating biological diversity. Our study demonstrates sympatric diversification of yeast starting from an isogenic population and provides detailed mechanistic insights into the factors and conditions responsible for generating and maintaining the population diversity.

Selection in a growing colony biases results of mutation accumulation experiments

Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 10⁸). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.

Mechanisms associated with the rapid decline in sea ice cover around a stranded ship in the Lazarev Sea, Antarctica

In the satellite data era starting from 1979, the extent of Antarctic sea ice increased moderately for the first 37 years. However, the extent decreased to record low levels from 2016 to 2020, with the drop being greatest in the Weddell and Lazarev Seas of the Southern Ocean. An important question for the scientific fraternity and policymakers is to understand what ocean-atmospheric processes triggered such a rapid decline in sea ice. We employ in-situ, satellite, and atmospheric reanalysis data to examine the causative mechanism of anomalous sea ice variability in the Lazarev Sea at a time of ice growth in the annual cycle (March-April 2019), when a cargo ship was stuck in extensive ice cover and freed following the unusual decline in sea ice. High-resolution Sentinel-1 synthetic aperture radar captured a distinct view of the ship location and track within extensive ice cover of fast sea ice, dense pack ice, and icebergs in the Lazarev Sea on 27 March 2019. Subsequently, the sea ice cover declined and reached the fourth lowest extent in the entire satellite record during April 2019 which was 25.6% lower than the long-term mean value of 2.65 × 10⁶ km². We show that the anomalous sea ice variability was due to the occurrence of eastward-moving polar cyclones, including a quasi-stationary explosive development that impacted sea ice through extreme changes in ocean-atmospheric conditions. The cyclone-induced dynamic (poleward propagation of ocean waves and ice motion) and thermodynamic (heat and moisture plumes from midlatitudes, ocean mixed layer warming) processes coupled with high tides provided a conducive environment for an exceptional decline in sea ice over the region of ship movement.

GAL Regulon in the Yeast S. cerevisiae is Highly Evolvable via Acquisition in the Coding Regions of the Regulatory Elements of the Network

GAL network in the yeast S. cerevisiae is one of the most well-characterized regulatory network. Expression of GAL genes is contingent on exposure to galactose, and an appropriate combination of the alleles of the regulatory genes GAL3, GAL1, GAL80, and GAL4. The presence of multiple regulators in the GAL network makes it unique, as compared to the many sugar utilization networks studied in bacteria. For example, utilization of lactose is controlled by a single regulator LacI, in E. coli’s lac operon. Moreover, recent work has demonstrated that multiple alleles of these regulatory proteins are present in yeast isolated from ecological niches. In this work, we develop a mathematical model, and demonstrate via deterministic and stochastic runs of the model, that behavior/gene expression patterns of the cells (at a population level, and at a single-cell resolution) can be modulated by altering the binding affinities between the regulatory proteins. This adaptability is likely the key to explaining the multiple GAL regulatory alleles discovered in ecological isolates in recent years.

Limited Pairwise Synergistic and Antagonistic Interactions Impart Stability to Microbial Communities

One of the central goals of ecology is to explain and predict coexistence of species. In this context, microbial communities provide a model system where community structure can be studied in environmental niches and in laboratory conditions. A community of microbial population is stabilized by interactions between participating species. However, the nature of these stabilizing interactions has remained largely unknown. Theory and experiments have suggested that communities are stabilized by antagonistic interactions between member species, and destabilized by synergistic interactions. However, experiments have also revealed that a large fraction of all the interactions between species in a community are synergistic in nature. To understand the relative significance of the two types of interactions (synergistic vs. antagonistic) between species, we perform simulations of microbial communities with a small number of participating species using two frameworks—a replicator equation and a Lotka-Volterra framework. Our results demonstrate that synergistic interactions between species play a critical role in maintaining diversity in cultures. These interactions are critical for the ability of the communities to survive perturbations and maintain diversity. We follow up the simulations with quantification of the extent to which synergistic and antagonistic interactions are present in a bacterial community present in a soil sample. Overall, our results show that community stability is largely achieved with the help of synergistic interactions between participating species. However, we perform experiments to demonstrate that antagonistic interactions, in specific circumstances, can also contribute toward community stability.

Experimental Evolution of Anticipatory Regulation in Escherichia coli

Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of Escherichia coli in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded via mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.

Molecular epidemiology of Burkholderia mallei isolates from India (2015-2016): New SNP markers for strain tracing

Glanders, caused by a bacterium called B. mallei, is primarily an infectious horse and human disease. Although its incidence is rare in developed countries, it is nonetheless prevalent in several geographical areas of the world. There is a lack of cost-effective, rapid and specific molecular typing tools for epidemiological tracing of glanders cases. We previously reported an SNP-based typing method that categorizes global B. mallei strains into three lineages (L1 to L3), as well as additional branches, sub-branches and groups. However, further discrimination of the Indian and Pakistani isolates within the L2B2sB2 sub-branch was not possible due to the lack of sufficient epidemiological markers. In this study, 10 B. mallei strains isolated from four states in India during 2015-2016 were whole genome sequenced; SNP analysis further confirmed their position in the L2B2sB2 branch. To better track the strains, four new markers targeting Indian or Pakistani strains, and specifically targeting sub-groups within the Indian strains, were identified. The new SNP markers were tested and validated on the 10 Indian isolates included in this study as well as on 6 contemporary B. mallei Pakistani strains. These rapid and discriminating typing tools will contribute to the epidemiological monitoring of B. mallei infections, particularly in South Asia and the Middle East, endemic regions of the disease.

Immunohistological localisation of growth factors in stroma and interstitial gland tissue of goat (Capra hircus) ovary

The growth factors platelet derived growth factor (PDGF), transforming growth factor alpha (TGF-α) and transforming growth factor beta (TGF-β) have been demonstrated to stimulate the in vitro prolife­ration of theca and granulosa cells in different animals. The present study was conducted to localise the growth factors PDGF, TGF-α and TGF-β in different types of interstitial cells and stromal cells of normal cycling goat ovaries. Tissue fixed in formalin was processed through a graded series of alcohols and embedded in paraffin wax. The sections were immunohistochemically stained with antibo­dies against PDGF, TGF-α and TGF-β. The binding affinity of interstitial cells and stromal cells were observed and photographed. The staining pattern of PDGF, TGF-α and TGF-β was mild to strong in stromal cells. The primary and secondary interstitial cells exhibited varied staining patterns for all studied growth factors. These findings in goat suggests that PDGF, TGF-α, TGF-β were potentially an important autocrine regulator of different cell functions and possibly a paracrine regulator of ovarian cell function at various development stages.

143 Therapeutic efficacy and safety of adipose tissue-derived mesenchymal stem cells in treating mastitis and metritis in dairy cattle

Mastitis and metritis are two inflammatory diseases with high economic impact on dairy industry and farmers are losing revenues. Antibiotic treatment for these disease conditions typically achieve suboptimal outcomes. Moreover, emerging antibiotic resistance in mastitis and metritis worldwide has a severe effect on productivity, fertility, and lifespan of animals. A paradigm shift in treatment strategies is much needed for these animals. Attracting properties of mesenchymal stem cells may act as an alternative strategy for treating these diseases. In addition to their ability to differentiate into multiple types of cells, mesenchymal stem cells can orchestrate immune responses and modulate tissue microenvironments. In the present study, we evaluated the safety and efficacy of adipose tissue–derived mesenchymal stem cells (AT-MSC) for mastitis and metritis. A well-characterised adipose-derived stem cell line with 3–5 passages cells were used for treatment for these diseases. In a safety trial, mastitis- and metritis-infected cattle were administered with 1×106 cells of AT-MSC through different routes (local, IV, IV+local). Animals were clinically evaluated during 15 days of the experimental period and blood samples were collected for hemogram determination. The efficacy was checked under both invivo and invitro conditions. Invitro efficiency of AT-MSC was determined using a transwell plate experiment, in which AT-MSC were co-cultured with bacteria (Escherichia coli and Staphylococcus). Invivo efficiency was evaluated by administration of in 2mL (1×106 cells) of AT-MSC dose; then, somatic cell count (SCC) in milk of mastitic cattle and polymorphonuclear (PMN) cell count in cervical vaginal fluid (CVF) of metritic cattle were determined. Gene expression profiling of antimicrobial (cathelicidin, lipocalin, cystatin) and anti-inflammatory (IL-4, IL-6, IL-10) peptides were quantified in all groups: IV, local, IV+local, and control ATB (antibiotic). Allogenic AT-MSC did not induce any immunological rejection response in treated animals. A significant reduction of bacteria in CVF invitro when co-cultured with AT-MSC was observed. The PMN count was significantly reduced in CVF of the IV+local group. The SCC in milk of mastitic animals was decreased in the local (intramammary) group. Maximum expression of IL-6, IL-10, cathelicidin, lipocalin, and cystatin and angiopoietin genes were observed on Day 3 followed by Day 7 in the local group in case of mastitis. In metritis, expression of IL-6, IL-10, cathelicidin, lipocalin, cystatin, and angiopoietin were observed at Day 3 in the IV+local group. All mastitic and metritic cattle were completely and permanently cured within 30 days after treatment with mesenchymal stem cells. In conclusion, we provide initial evidence for the use of allogenic AT-MSC and their safety and efficacy to treat mastitis and metritis in dairy cattle.

Practical consensus recommendations regarding the management of sentinel lymph node issues in early breast cancer

Axillary lymph node involvement is a very important poor prognostic factor in the clinical staging and management of breast cancer patients. Traditionally, axillary lymph node dissection (ALND) has been used for determining the status of the axillary lymph nodes. More recently the sentinel lymph node biopsy (SLNB) procedure has gained wider acceptance as the standard of care, having the advantage of being less invasivewhile providing good accuracy. This expert group used data from published literature, practical experience and opinion of a large group of academic oncologists to arrive at these practical consensus recommendations in regards with the use of the two different procedures and other issues in patients with early breast cancer for the benefit of community oncologists.

Phenotypic Heterogeneity in Tumor Progression, and Its Possible Role in the Onset of Cancer

Heterogeneity among isogenic cells/individuals has been known for at least 150 years. Even Mendel, working on pea plants, realized that not all tall plants were identical. However, Mendel was more interested in the discontinuous variation between genetically distinct individuals. The concept of environment dictating distinct phenotypes among isogenic individuals has since been shown to impact the evolution of populations in numerous examples at different scales of life. In this review, we discuss how phenotypic heterogeneity and its evolutionary implications exist at all levels of life, from viruses to mammals. In particular, we discuss how a particular disease condition (cancer) is impacted by heterogeneity among isogenic cells, and propose a potential role that phenotypic heterogeneity might play toward the onset of the disease.

DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

Next-generation sequencing (NGS) technologies have provided affordable but errorful ways to generate raw genetic data. To extract variant information from billions of NGS reads is still a daunting task which involves various hand-crafted and parameterized statistical tools. Here we propose a deep neural networks (DNN) based alignment and single nucleotide variant (SNV) identifier tool known as DAVI: deep alignment and variant identification. DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species. The use of DAVI will therefore help non-human sequencing projects to benefit from the wealth of human ground truth data. Moreover, this approach is a migration from expert-driven statistical models to generic, automated, self-learning models.

84 Folate-methionine cycle and folate transport in developing buffalo embryos

Periconceptional folic acid is known to have a major role in the prevention of neural tube defects, leading to global recommendations for folic acid supplementation before and in early pregnancy. Maternal folate throughout pregnancy may have other roles in offspring health, including neurodevelopment and cognitive performance in childhood. Folate and folic acid (vitamin B9) act as a co-enzyme essential for single carbon metabolism, a network of pathways involved in several biological processes including nucleotide synthesis, DNA repair, and methylation reactions. In general, rapidly growing and multiplying cells require an adequate supply of folate. A primary deficiency of natural folate resulting in an increase of the total homocysteine concentration may be detrimental to the quality of the oocyte, subsequent fertilisation, embryogenesis, implantation, and fetal development. However, to date, folate-methionine metabolism and folate transport have not been studied in developing buffalo embryos. The present study details transcript expression for genes encoding key enzymes in the linked folate-methionine cycles in the ovary tissue, cumulus cells, immature oocytes, IVM oocytes, and pre-implantation embryos and also estimates the folate concentration in follicular fluid (FF) of buffalo. The FF was pooled and collected by aspiration of different sizes of surface follicles (2-8mm diameter). The total number of analysed samples was three, with different dilutions and estimation of folate in FF of buffalo done by chemiluminescence assay. Total RNA was extracted from oocytes, cumulus cells, ovarian tissue, and embryos produced from IVF. RT-PCR was performed to analyse the expression of folate-methionine cycle enzymes and folate transporters. Transcripts for all the enzymes of the folate-methionine cycle (i.e. SHMT, MTR, MTRR, MAT1A, MAT2B, GNMT, AHCY, CBS, and DHFR) and folate transporters (FOLR1, FOLR2) and reduced folate carrier (SLC19A1) were expressed in ovarian tissue, cumulus cells, oocytes, and pre-implantation embryos. Immunocytochemical analysis revealed FOLR2 and SLC19A1 protein expression on the plasma membrane and/or cytoplasm of the oocytes and embryos, and FOLR1 in the nucleus of pre-implantation embryos. The folate concentration in FF was 24ngmL−1. This is the first report to examine the concentration of folate in FF and revealed the identification of transcripts in different samples of buffalo species. The presence of these enzymes could have a profound effect on single-carbon metabolism within the ovary and pre-implantation embryo, therefore indicating that folate from FF is being disseminated through folate receptors within oocytes and embryos to participate in the folate pathway. This study advocates the necessity for examination of the result of folate supplementation throughout invitro embryo production for improving the quality and quantity of transferable blastocysts and subsequently live calf births in buffalo.

220 Exploring the use of mesenchymal stem cells for treatment of mastitis and metritis in cattle

The present study was carried out to isolate mesenchymal stem cells (MSCs) from adipose tissue of cattle (Bos indicus), characterise them, and apply them for the treatment of mastitis and metritis in the cow. Cattle MSCs were isolated from adipose tissue near the loin region of cow. Isolated adipose tissue was subjected to enzymatic digestion using 2% collagenase with agitation at regular intervals. The cells obtained after digestion were resuspended in cell culture flasks containing growth enriched medium and cultured under standard culture conditions. Alkaline phosphatase staining was used as one of the parameters to confirm cultured putative MSCs. Bovine Ad-MSCs were further characterised using real time-PCR by amplification of MSC-specific markers: CD73, CD90, and CD105 as positive markers and CD34, CD45, and CD79a as negative markers. Immunocytochemistry showed the presence of CD73, CD90, and CD105 on the cell surface. Three groups-control (C), local (L), and intravenous (IV)-with 6 cows suffering from mastitis were taken in each group and subjected to MSC transplantation through local and intravenous routes. Control group animals were subjected to antibiotic treatment only. Similarly, another three groups were taken with 6 cows in each group suffering from metritis. Post-transplantation wound healing, tissue repair, and reduction in inflammation were monitored for 26 days, at different time intervals; that is, after Days 1, 3, 7, and 15. Blood samples were also collected from animals at the same time intervals for real time-PCR. A similar examination was also done in metritis groups along with the analysis of the reduction in turbidity of cervical fluid at the abovementioned time intervals. Real time-PCR was performed to determine relative expression of genes for proliferative factors, anti-inflammatory cytokines, and antimicrobial peptides on cells isolated from blood collected at different time intervals. Gene expression in the local group of mastitis subjected to MSC injection was significantly higher than that of the IV and control group. The somatic cell count declined in both local and IV groups compared with the control group. Whereas the expression of the same genes in the IV group of metritis was significantly higher than that of the local and control groups of cows. The turbidity of cervical fluid and mucus was reduced in the IV group compared with the local group. In conclusion, we demonstrated the healing potential of MSCs in a cow model via MSC injection. Promising results were obtained in curing mastitis in both local and IV groups, whereas healing in the case of metritis was significantly higher in the IV group compared with both the control and local groups of cows. The study indicates the potential use of MSc for treatment of mastitis and metritis in cattle through wound healing and decreasing microbial infection.

Evolution of Escherichia coli in different carbon environments for 2,000 generations

Cellular energetics is thought to have played a key role in dictating all major evolutionary transitions in the history of life on Earth. However, how exactly cellular energetics and metabolism come together to shape evolutionary paths is not well understood. In particular, when an organism is evolved in different energy environments, what are the phenomenological differences in the chosen evolutionary trajectories, is a question that is not well understood. In this context, starting from an Escherichia coli K-12 strain, we evolve the bacterium in five different carbon environments-glucose, arabinose, xylose, rhamnose and a mixture of these four sugars (in a predefined ratio) for approximately 2,000 generations. At the end of the adaptation period, we quantify and compare the growth dynamics of the strains in a variety of environments. The evolved strains show no specialized adaptation towards growth in the carbon medium in which they were evolved. Rather, in all environments, the evolved strains exhibited a reduced lag phase and an increased growth rate. Sequencing results reveal that these dynamical properties are not introduced via mutations in the precise loci associated with utilization of the sugar in which the bacterium evolved. These phenotypic changes are rather likely introduced via mutations elsewhere on the genome. Data from our experiments indicate that evolution in a defined environment does not alter hierarchy in mixed-sugar utilization in bacteria.

Phenomenological models as effective tools to discover cellular design principles

Microbes have proved useful to us in many different ways. To utilize microbes, we have mostly focused on maximizing growth, to improve yield of chemicals derived from the microbes. However, to truly tap into their potential, we should also aim to understand microbial physiology. We present a historical perspective of the developments in the field of Microbial Biotechnology, focusing on how the growth-modelling approaches have changed. Starting from simple empirical growth models, we have evolved towards mechanistic and phenomenological models which use molecular and physiological details to drastically improve prediction power of these models. Lastly, we explore the as of yet unsolved questions in microbial physiology, and discuss how the ability to monitor microbial growth at single cell resolution using the lab-on-a-chip technologies is uncovering previously unobservable causal principles underlying microbial growth.

Mathematical modeling of movement on fitness landscapes

Background

Movement of populations on fitness landscapes has been a problem of interest for a long time. While the subject has been extensively developed theoretically, reconciliation of the theoretical work with recent experimental data has not yet happened. In this work, we develop a computational framework and study evolution of the simplest transcription network between a single regulator, R and a single target protein, T.

Results

Through our simulations, we track evolution of this transcription network and comment on its dynamics and statistics of this movement. Significantly, we report that there exists a critical parameter which controls the ability of a network to reach the global fitness peak on the landscape. This parameter is the fraction of all permissible values of a biochemical parameter that can be accessed from its current value via a single mutation.

Conclusions

Overall, through this work, we aim to present a general framework for analysis of movement of populations (and particularly regulatory networks) on landscapes.

Electronic supplementary material

The online version of this article (10.1186/s12918-019-0704-0) contains supplementary material, which is available to authorized users.

Long-term outcome of trans-sphenoidal surgery for Cushing's disease in Indian patients

BACKGROUND

The results of trans-sphenoidal surgery (TSS) in Cushing's disease (CD) vary widely depending upon patient characteristics as well as surgical experience. Patients in India are often referred late to referral centers. We studied the rates of remission and endocrine deficiencies after TSS in patients with CD presenting to a referral hospital in India.

METHODS

Sixty consecutive patients (45 females, median age 24.5 years) who underwent TSS between 2000 and 2015 were studied. The median (range) duration of follow-up was 40 (3-138) months. Initial and long-term remission and relapse rates and pituitary hypofunction post-TSS were evaluated.

RESULTS

Eighteen (30%) patients harbored macroadenomas. Twenty-eight (47%) patients achieved remission in the immediate post-operative period (8 AM serum cortisol < 140 nmol/l), while a higher remission rate was noted at 6 months (39/54 patients, 72%). At 1 year 70% patients and at final follow-up [median duration 40 (range 3-138) months], 58% of patients were in remission. No pre- or post-surgical variables were consistently associated with remission, except for the 8-AM serum cortisol level on the fifth day after surgery. Seven (18%) patients relapsed on follow-up, including five patients who had fifth post-operative day 8 AM serum cortisol < 140 nmol/l. Twelve (25%) patients newly developed hypothyroidism and one (1.6%) patient developed amenorrhoea after TSS.

CONCLUSION

Remission rate at 6 months was higher than immediately after TSS. A significant proportion of patients relapsed, thus necessitating life-long follow-up. New-onset hypothyroidism was frequent after TSS.

Dynamics and Control of Flagella Assembly in Salmonella typhimurium

The food-borne pathogen Salmonella typhimurium is a common cause of infections and diseases in a wide range of hosts. One of the major virulence factors associated to the infection process is flagella, which helps the bacterium swim to its preferred site of infection inside the host, the M-cells (Microfold cells) lining the lumen of the small intestine. The expression of flagellar genes is controlled by an intricate regulatory network. In this work, we investigate two aspects of flagella regulation and assembly: (a) distribution of the number of flagella in an isogenic population of bacteria and (b) dynamics of gene expression post cell division. More precisely, in a population of bacteria, we note a normal distribution of number of flagella assembled per cell. How is this distribution controlled, and what are the key regulators in the network which help the cell achieve this? In the second question, we explore the role of protein secretion in dictating gene expression dynamics post cell-division (when the number of hook basal bodies on the cell surface is reduced by a factor of two). We develop a mathematical model and perform stochastic simulations to address these questions. Simulations of the model predict that two accessory regulators of flagella gene expression, FliZ and FliT, have significant roles in maintaining population level distribution of flagella. In addition, FliT and FlgM were predicted to control the level and temporal order of flagellar gene expression when the cell adapts to post cell division consequences. Further, the model predicts that, the FliZ and FliT dependent feedback loops function under certain thresholds, alterations in which can substantially affect kinetics of flagellar genes. Thus, based on our results we propose that, the proteins FlgM, FliZ, and FliT, thought to have accessory roles in regulation of flagella, likely play a critical role controlling gene expression during cell division, and frequency distribution of flagella.