Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

Non-Gaussian numerical errors versus mass hierarchy

We probe the numerical errors made in renormalization group calculations by varying slightly the rescaling factor of the fields and rescaling back in order to get the same (if there were no round-off errors) zero momentum 2-point function (magnetic susceptibility). The actual calculations were performed with Dyson's hierarchical model and a simplified version of it. We compare the distributions of numerical values obtained from a large sample of rescaling factors with the (Gaussian by design) distribution of a random number generator and find significant departures from the Gaussian behavior. In addition, the average value differ (robustly) from the exact answer by a quantity which is of the same order as the standard deviation. We provide a simple model in which the errors made at shorter distance have a larger weight than those made at larger distance. This model explains in part the non-Gaussian features and why the central-limit theorem does not apply.Comment: 26 pages, 7 figures, uses Revte

Monitoring drinking water quality in South Africa: Designing information systems for local needs

In South Africa, the management and monitoring of drinking water quality is governed by policies and regulations based on international standards. Water Service Authorities, which are either municipalities or district municipalities, are required to submit information regarding water quality and the management thereof regularly to the national Blue Drop System (BDS). Since 2009, a trend has emerged in which urban municipalities have been shown to consistently improve their water quality management whilst some of the rural and under-resourced municipalities are falling behind. A major concern has been that rural municipalities are failing to report the required information and are not complying with some of the regulator’s requirements that speak to the overall management of water quality monitoring rather than the actual water quality itself. This paper reflects on a case study undertaken in four rural municipalities in South Africa where a cellphone-based information system was implemented to collect information relevant to the municipality. The study was conducted by the Information for Community Oriented Municipal Services (iCOMMS) research team based at the Department of Civil Engineering at the University of Cape Town. The hypothesis for the research was that improved information flow within rural municipalities – from water supplies in outlying areas to the municipal government office – can improve the efficiency of existing monitoring, if the design, development and implementation of such a system are based on collecting appropriate and locally relevant information. Water service authorities at the four field sites managed the process of monitoring in very different ways due to limited resources as well as structural challenges within each government department. The variety of stakeholders involved in water quality monitoring programmes, and the alternative methods and processes used, challenges the current understanding of information system design as well as the notion of developing a single national information system. The decentralisation of national water quality monitoring to municipal level was assessed in this research, which concluded that the BDS was of limited usefulness to water quality monitoring in the rural municipalities partaking in this research.Keywords: water quality monitoring, information management, Blue Drop System, decentralisation, rural municipalitie

Finger patterns produced by thermomagnetic instability in superconductors

A linear analysis of thermal diffusion and Maxwell equations is applied to study the thermomagnetic instability in a type-II superconducting slab. It is shown that the instability can lead to formation of spatially nonuniform distributions of magnetic field and temperature. The distributions acquire a finger structure with fingers perpendicular to the screening current direction. We derive the criterion for the instability, and estimate its build-up time and characteristic finger width. The fingering instability emerges when the background electric field is larger than a threshold field, $E>E_c$, and the applied magnetic field exceeds a value $H_fing \propto 1/\sqrt{E}$. Numerical simulations support the analytical results, and allow to follow the development of the fingering instability beyond the linear regime. The fingering instability may be responsible for the nucleation of dendritic flux patterns observed in superconducting films using magneto-optical imaging.Comment: 8 pages, 6 figures, accepted to Phys. Rev. B; (new version: minor changes

Field Identification of Major Elasmobranchs along the Indian Coast

Elasmobranchs are an important group of demersal fishes which are represented by sharks, skates and rays. India is the world’s second biggest shark fishing nation next to Indonesia. They belong to the Class Elasmobranchii under the Phylum Chordata. Sharks are caught with various gears like drift gillnets, longlines, hooks and line units and are landed throughout the year. They feed on bony fishes, other sharks, rays, crustaceans and squids

Tracing the sites of obscured star formation in the Antennae galaxies with Herschel-PACS

FIR imaging of interacting galaxies allows locating even hidden sites of star formation and measuring of the relative strength of nuclear and extra-nuclear star formation. We want to resolve the star-forming sites in the nearby system of the Antennae. Thanks to the unprecedented sharpness and depth of the PACS camera onboard ESA's Herschel Space Observatory, it is possible for the first time to achieve a complete assessment of individual star-forming knots in the FIR with scan maps at 70, 100, and 160 um. We used clump extraction photometry and SED diagnostics to derive the properties related to star-forming activity. The PACS 70, 100, and 160 um maps trace the knotty structure of the most recent star formation along an arc between the two nuclei in the overlap area. The resolution of the starburst knots and additional multi-wavelength data allow their individual star formation history and state to be analysed. In particular, the brightest knot in the mid-infrared (K1), east of the southern nucleus, exhibits the highest activity by far in terms of dust heating and star formation rate, efficiency, and density. With only 2 kpc in diameter, this area has a 10-1000 um luminosity, which is as high as that of our Milky Way. It shows the highest deficiency in radio emission in the radio-to-FIR luminosity ratio and a lack of X-ray emission, classifying it as a very young complex. The brightest 100 and 160 um emission region (K2), which is close to the collision front and consists of 3 knots, also shows a high star formation density and efficiency and lack of X-ray emission in its most obscured part, but an excess in the radio-to-FIR luminosity ratio. This suggests a young stage, too, but different conditions in its interstellar medium. Our results provide important checkpoints for numerical simulations of interacting galaxies when modelling the star formation and stellar feedback.Comment: 4 pages, 4 figures, 2 tables (A&A Herschel special issue

Decadal Trends of Indian Demersal Fisheries

Fisheries sector plays an important role in the overall socio-economic development of India. India is one of the major fish producing countries in the world contributing over 3% of both marine and freshwater fishes of the world production. Marine fishes, based on their depth-wise distribution are grouped mainly as pelagic and demersal, the former occupying surface and subsurface waters and the latter the neritic areas in the continental shelf. Demersal fishes are those fishes which can either rest on the sea floor or which can float in the water column just above the sea floor. The demersal fish resources of India include the elasmobranchs, eels, major perches, threadfin breams, silverbellies, sciaenids, lizardfishes, pomfrets, bulls eye, catfishes, flatfishes, goatfish and white fish. There is a significant contribution by the demersal fishes to the total Indian marine fish landings. When compared to the pelagic resources, proper exploitation of the demersal finfishes in India has been initiated since 1960-62 period. With the introduction of mechanized bottom trawling the exploitation of demersal finfishes attained a 2.7 fold increase reaching 0.52 million tonnes in the late eighties from 0.08million tonnes during the late fifties. In 2017, the demersal fish production of India reached new heights with a peak annual average landing of 1 million tonne which is almost an increase of 12.5 fold from the late fifties. The annual average landings of demersal finfishes along the Indian coast during 2010-2015 was accounted to 0.95 million tonnes contributing 26.32% to the total landings. However, the catch share of demersal finfishes during the last 35 years indicates that the contribution of demersal finfishes to the total Indian marine landings is decreasing over the years. The maximum share was reported in 1983 with 33% contribution and the lowest share was in 1989

Field Identification of Major Demersal Teleost Fish Species along the Indian Coast

Based on their vertical distribution, fishes are broadly classified as pelagic or demersal. Species those are distributed from the seafloor to a 5 m depth above, are called demersal and those distributed from a depth of 5 m above the seafloor to the sea surface are called pelagic. The term demersal originates from the Latin word demergere, which means to sink. The demersal fish resources include the elasmobranchs, major perches, catfishes, threadfin breams, silverbellies, sciaenids, lizardfishes, pomfrets, bulls eye, flatfishes, goatfish and white fish. This chapter deals with identification of the major demersal teleost fish species

Climate Change Impacts on Indian Marine Fisheries and adaptation strategies

Increase in greenhouse gases (GHGs) in the atmosphere has resulted in warming of climate systems or global warming. Global warming is a long-term rise in the average temperature of the earth's climate system, an aspect of climate change shown by temperature measurements and by multiple effects of the warming. The term commonly refers to the mainly human-caused observed warming since pre-industrial times and its projected continuation, though there were also much earlier periods of global warming. In the modern context the terms are commonly used interchangeably, but global warming more specifically relates to worldwide surface temperature increases; while climate change is any regional or global statistically identifiable persistent change in the state of climate which lasts for decades or longer, including warming or cooling. Many of the observed warming changes since the 1950s are unprecedented in the instrumental temperature record and in historical and paleoclimate proxy records of climate change over thousands to millions of years