Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Trend of malaria incidences and its association with rainfall in Kalahandi District of Odisha, India

In Odisha, Kalahandi is one of the most exposed and vulnerable districts to malaria incidences due to its poor socioeconomic condition and extreme climate. The study aimed to explore the temporal characteristics of malaria incidences in Kalahandi and to identify its relationship with rainfall for the period from 2011 to 2018. Out of the total blood films examined, 8.84% were found positive in Kalahandi between 2011 and 2018. Plasmodium falciparum is the most dominant species accounted 88.3% of the total cases. Very high mean annual parasitic index (API) >15 is recorded throughout the study years. The highest incidences are recorded in the monsoon season followed by postmonsoon. The correlation value of the annual blood examination rate with P. falciparum, Plasmodium vivax, and API has shown a very high positive correlation. Rainfall shows a (+) correlation with malaria incidences in the cold (0.47) and hot seasons (0.01) and (-) correlation in the monsoon (-0.54) and postmonsoon season (-0.54).

Integrated remote sensing and field-based approach to assess the temporal evolution and future projection of meanders: A case study on River Manu in North-Eastern India

A common phenomenon associated with alluvial rivers is their meander evolution, eventually forming cutoffs. Point bar deposits and ox-bow lakes are the products of lateral bend migration and meander cutoff. The present study focuses on identifying the meanders of River Manu and their cutoffs. Moreover, this study compares the temporal evolution and predicts the progress of selected meanders of River Manu. In the present research, the Survey of India topographical map, satellite imagery, and geographic information system (GIS) technique were used to examine the evolution of the Manu River meander. Subsequently, a field visit was done to the selected cutoffs and meanders of River Manu to ascertain the present status and collect data. It has been observed that many cutoffs have undergone temporal changes, and their sizes have decreased. Some have become dried or converted to agricultural fields. The width of River Manu has decreased in all the selected bends from 1932 to 2017. The sinuosity index has changed from 2.04 (1932) to 1.90 (2017), and the length of the river has decreased by 7 km in 85 years (1932–2017). The decrease in length is evident from lowering the number of meanders. Uniformity coefficient and coefficient of curvature of the bank soil samples were calculated, indicating that the soil is poorly graded and falls under the cohesionless category. Based on cross-section analysis, sediment discharge, grain-size analysis of the bank material, channel planform change, and radius of curvature, it can be stated that almost all the selected bends have the probability of future cutoff. The highest probabilities were observed in bend 3 (Jalai) and bend 4 (Chhontail). This work is aimed to provide planners with decisions regarding the construction of roads and bridges in areas that show the huge dynamicity of river meandering.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

Climate and Disease vulnerability analysis in blocks of Kalahandi District of Odisha, India

BACKGROUND

Diarrhea and typhoid, ancient water-borne diseases which are highly connected to rainfall are serious public health challenges in the blocks of Kalahandi district of Odisha, India.

OBJECTIVES

Corroboration of rainfall and waterborne diseases are available in abundance; therefore, the objective of this article is to calculate the climate and disease vulnerability index (CDVI) value for each block of Kalahandi.

METHODS

We have applied the livelihood vulnerability index with some modifications and classify the three major categories, i.e., exposure, sensitivity, and adaptive capacity into six subcategories. These six subcategories are further divided into 26 vulnerability indicators based on a detailed literature review.

RESULTS

The result indicated that the Thuamul Rampur block, the southernmost part of the district is highly exposed to the annual and seasonal mean rainfall, and the Madanpur Rampur block lies in the northernmost part of the district is highly exposed to diarrhea and typhoid. Based on the calculation of the final CDVI value, nearly 50% of blocks of the Kalahandi district fall in the category of very high to high vulnerable zones. Furthermore, it has been observed that factors such as rainfall and disease distribution, vulnerable population and infrastructure, and education and health-care capacities had a notable influence on vulnerability.

CONCLUSION

It is rare to find a health vulnerability-related study in India at this microlevel based on the suitable indicators selected for a tribal and backward region.

Assessing Waterborne Disease Vulnerabilities in the Blocks of Kalahandi District of Odisha, India

Background:

Outbreaks of waterborne diseases caused by the contamination of water in the rural and tribal regions have become an area of prime concern in the research arena. The impact and intensity of waterborne diseases are expected to increase in these socioeconomic backward regions.

Objective:

The purpose of the study is to calculate the waterborne disease vulnerability index (DVI) for 13 blocks of the Kalahandi district of Odisha. Diarrhea and typhoid are two major diseases prevailing in each block of the district.

Materials and Methods:

Livelihood vulnerability index has been applied with some modifications to calculate the DVI for each block. In the DVI calculation, diseases are taken as an indicator for the exposure section. The sensitivity and adaptive capacity sections are categorized into two subcomponents to study the vulnerability of each block.

Results:

We have observed uneven distribution of diarrhea and typhoid among the blocks of Kalahandi. The result indicates that vulnerable populations and infrastructure play an important role in enhancing vulnerability whereas educational and health-care capacity reduces its impact. We have found that more than 50% of blocks in the district are categorized in moderate to high vulnerable zones.

Conclusion:

This study is done to understand the relationship between disease exposure, related vulnerability, and adaptive capacity. It is unique in the way the indicators have been chosen in the proposed method for the calculation of DVI and will have a higher degree of practical applicability.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Spatiotemporal evaluation of water quality incidents in Japan between 1996 and 2007

We present a spatiotemporal evaluation of water quality incidents in Japan considering incident numbers, incident causes, pollutant categories, and pollution effects. Water pollution incidents in first-class river systems almost tripled to about 1487 in the 12 years from 1996 to 2007. In addition, oil makes up the largest proportion of pollutants nationwide (76.61%) and the major source of pollution for each region in Japan. Moreover, every category shows a growth trend, especially since 2005. The main cause of incidents was "Unknown" (43%), followed by "Poor working practice" (24%), and then by "Accident" (10%) and "Other" (10%). In Hokuriku, however, the main cause of incidents was "Poor working practice" (36%), which is greater than "Unknown" (30%). Finally, waterworks (approximately 60%) was the largest of four kinds of water supply infrastructure affected by pollution incidents, followed by simplified waterworks. The population affected by offensive odors and tastes peaked in 1990 and has been decreasing. Overall, the results show the characteristics of incidents from 1996 to 2007, with significant implications for adaptation measures, strategies and policies to reduce water quality incidents.

Production of melanin pigment from Pseudomonas stutzeri isolated from red seaweed Hypnea musciformis

Hypnea musciformis red seaweed is popularly known to produce carrageenan was collected from the Gulf of Mannar, India. Strain HMGM-7 [MTCC 11712] was isolated from the surface of this seaweed, which was capable of producing an extracellular black-coloured polymeric pigment. Based on phenotypic characterization and 16S rDNA sequencing, the strain HMGM-7 was identified as Pseudomonas stutzeri. Biophysical characterization by UV-visible, FT-IR, EPR and XRD spectroscopic studies confirmed the pigment as melanin. Further chemical characterization showed that it was acid-resistant, alkali-soluble and alkali-insoluble in most of the organic solvents and distilled water. To our knowledge, this is a first report on a marine Pseudomonas stutzeri strain producing significant amounts of melanin of about 6·7 g l(-1) without L-tyrosine supplementation in the sea-water production medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This investigation reports a marine Pseudomonas stutzeri strain HMGM-7 [MTCC 11712] that produces significant quantities of melanin (6·7 g l(-1) ) in sea-water medium without the supplementation of L-tyrosine. The confirmation of the produced melanin was carried out by various chemical and physical characterization studies. The isolated melanin may find potential application for use in cosmetic and/or pharmaceutical industries.

Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition

The crystal structure of Fab of an Ab PC283 complexed with its corresponding peptide Ag, PS1 (HQLDPAFGANSTNPD), derived from the hepatitis B virus surface Ag was determined. The PS1 stretch Gln2P to Phe7P is present in the Ag binding site of the Ab, while the next three residues of the peptide are raised above the binding groove. The residues Ser11P, Thr12P, and Asn13P then loop back onto the Ag-binding site of the Ab. The last two residues, Pro14P and Asp15P, extend outside the binding site without forming any contacts with the Ab. The PC283-PS1 complex is among the few examples where the light chain complementarity-determining regions show more interactions than the heavy chain complementarity-determining regions, and a distal framework residue is involved in Ag binding. As seen from the crystal structure, most of the contacts between peptide and Ab are through the five residues, Leu3-Asp4-Pro5-Ala6-Phe7, of PS1. The paratope is predominantly hydrophobic with aromatic residues lining the binding pocket, although a salt bridge also contributes to stabilizing the Ag-Ab interaction. The molecular surface area buried upon PS1 binding is 756 A(2) for the peptide and 625 A(2) for the Fab, which is higher than what has been seen to date for Ab-peptide complexes. A comparison between PC283 structure and a homology model of its germline ancestor suggests that paratope optimization for PS1 occurs by improving both charge and shape complementarity.

Effect of thyroxine (T4) and thiourea on the hepatic oxygen consumption of male garden lizards of three different age groups

Administration of T4 (1 microgram/g body-weight on alternate days) to male garden lizards of three different age groups (young, middle-aged and old) for a period of 2 weeks caused a significant rise in the hepatic oxygen consumption, the degree of response increasing with advancing age. On the other hand, when treated in vitro (5 micrograms T4 in the medium) the stimulation of hepatic oxygen consumption was observed only in lizards of the young age group. Oral administration of thiourea (0.05 mg/g body-weight on alternate days, three doses) led to a decrease in hepatic oxygen uptake, the degree of inhibition being higher in young (30%) and old (28%) than in middle-aged lizards (12%).

Age-related changes in the response of hepatic succinic dehydrogenase activity to thyroxine and thiourea in lizards

Intraperitoneal injection of thyroxine (T4; 1 microgram/g body weight on alternate days, seven doses) to male garden lizards of three different age groups caused a stimulation of hepatic succinic dehydrogenase activity, the degree of response being higher in the old (63%) than in middle-aged (39%) and young (31%). Percent inhibition of enzyme activity following thiourea treatment (0.05 mg/g body weight on alternate days, three doses) was higher in middle-aged lizards (24%) than in young (10%) and old (12%) ones.