bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution of picoplankton and detritus in the lower course of the Kama River
Authors: Krasnova E S , Umanskaya M V
Published: July 2021

The distribution of picoplankton and detritus in the lower course of the Kama River in 2009, 2012, 2016 and 2020 was analyzed. The abundance (1.5-6.7 × 106cells mL−1) and biomass (25-173ug C L−1) of picoplankton corresponds to the mesotrophic level. The abundance and biomass of the heterotrophic picoplankton increases from spring to autumn, the autotrophic picoplankton has maximum in August. The amount (17-1367 × 103particles mL−1) and mass (0.1-62 μg C L−1) of picodetritus varies greatly from station to station without clear patterns, but basically its mass is higher at coastal stations. Heterotrophic picoplankton prevails in picoseston structure; the average APP and picodetritis contributions are comparable, with little excess of picodetritus. The structure of the picoseston varies significantly depending on the season and the riverbed or the coastal location of the station. The amount of nanodetritus is very high (up to 229 × 103particles mL−1and 662 μg C L−1), and it varies slightly both in space and in time. Its mass is almost always several times higher than the biomass of picoceston Most likely, nanodetritus is one of the main factors affecting the plankton of the lower course of the Kama River.
The current state of the steppe vegetation classification system in the Volga region
Authors: Lysenko T M
Published: July 2021

Steppe vegetation in the Volga region is one of the predominant types of vegetation. At present, it has survived only in areas inconvenient for human economic and recreational activities. Its research is necessary to understand the structure and composition of zonal vegetation and distribution patterns to predict changes in the modern vegetation cover. The relevance of studying the steppe vegetation of the Volga region is also due to the creation of the project “Vegetation of Russia”. We studied the steppe vegetation of the Volga region in the period from 2011 to 2020 from the standpoint of the J. Braun-Blanquet approach. Field studies covered all the diversity of the steppe vegetation represented in the region-herb-rich grass steppes, herb-grass steppes, grass steppes and desert and their psammophytic, petrophytic and halophytic edaphic variants within Ulyanovsk, Penza, Samara, Saratov, and Volgograd Oblasts, the western part of Orenburg Oblast and the northern part of Astrakhan Oblast. The syntaxonomic analysis of our own materials and literature data made it possible to establish 65 associations, 47 subassociations and 2 variants. They are assigned to the class Festuco-Brometea, the orders Festucetalia valesiacae, Helictotricho-Stipetalia, Tanaceto achilleifolii-Stipetalia lessingianae and the alliances Festucion valesiacae, Agropyrion pectinati, Centaureion sumensis, Stipion korshinskyi and Tanaceto achilleifolii-Stipion lessingianae.
Freshwater mollusks of the Priplotinny Ples Reach, the Kuibyshev Reservoir (middle Volga River, Russia)
Authors: Mikhailov R A
Published: July 2021

In September 2020, the fauna of mollusks was studied at the Priplotinny Ples Reach of the Kuibyshev Reservoir, the Volga River, Russia. In total, 23 taxa were registered, including four invasive species. Extrapolating of the species richness, taking into account the sampling effort, allowed to assess the estimated species pool according to the Chao 2 algorithm. Bivalve mollusks predominated in the studied area. The mollusks Dreissena (Pontodreissena) bugensis and Dreissena (Dreissena) polymorpha have been found most frequently at the study sites. Both abundance and biomass varied in wide range, as 391 ± 325 ind. m−2 and 256.693 ± 228.355 g m−2, respectively. The complex of dominant species was mainly represented by alien mollusks. The type of bottom sediment was a significant ecological factor (p ≤ 0.05) that determined the distribution of mollusks at the Priplotinny Ples Reach. The water quality of the study area was assessed by bioindication method according to the composition and structure of the mollusk fauna, formed mainly by species of European and European-West Siberian ranges.
Primary signs of internal organ diseases in carp in case of standard condition violations in fish farming ponds
Authors: Mineev A K , Mineeva O V
Published: July 2021

Hematological and histopathological study results of adult carp from a private fish farm are presented. Abnormalities in the main hematological parameters (blood elements ratio, leukocyte formula, erythropoiesis level, possible pathologies of erythrocytes) were not revealed. One third of the examined fish were found to have abnormalities in the tissues of gills, liver, and heart muscle in the form of minor focal formations (detachment of the gill epithelium, dissection of myofibrils, disorders of glycogen metabolism, foci of necrosis and infiltration) which indicates the initial stage of the pathological process. Kidneys, gonads, and somatic muscle fibers showed no signs of pathology. The main factors determining the primary signs of internal organ diseases are water quality (water saturated with magnesium, calcium, and iron salts, increased hardness) and an unbalanced diet (primarily, an insufficient amount of raw protein) that does not meet the standards adopted in fish farming. The registered initial signs of the pathological process in the gills, liver and heart muscle can be leveled by improving the carp keeping conditions.
Influence of Chloride- and Soda-Dominated Salinity on Physiological and Biochemical Aspects of Halophytes with Different Strategies of Salt Metabolism
Authors: Nesterov V N , Bogdanova E S
Published: July 2021

The authors study the effect of NaCl and NaHCO3 at concentrations of 1 M on the physiological and biochemical state of Salicornia perennans and Artemisia santonica for 24 hours. In our experiment, we evaluated: the accumulation of Na in the aerial part of plants, the stress index is lipid peroxidation (LPO); the state of membranes – by the composition and content of lipids and proteins, the level of photosynthetic pigments. The euhalophyte S. perennans accumulated Na on average 30% more than the glycohalophyte A. santonica. The addition of NaCl and NaHCO3 to the root environment promoted an increase in LPO in S. perennans by 2.4 times as compared to the control. In the case of A. santonica, LPO concentration increased by 1.2 times, but only when NaHCO3 was added to the soil. In addition, NaCl and NaHCO3 negatively affected plant lipids and proteins. Thus, in S. perennans plants, NaCl contributed to a decrease in phosphlipids by 34%, and NaHCO3 in glycolipids by 22% in comparison with the control. The quantitative content of the sum of water-soluble and membrane-bound proteins in the studied plants decreased by 10–36%. Chloride and soda-dominated salinity caused a decrease in the proportion of chlorophyll a and carotenoids only in S. perennans. The authors concluded that the response of the photosynthetic system and membrane complexes to various types of salinity in euhalophyte and glycohalophyte was different.
Analyzing Water Conservation Indicators in Russia
Authors: Rashoyan I I
Published: July 2021

The authors collected and analyzed statistical indicators of the use and pollution of water resources in Russia for the time period 2009-2019. The authors studied the dynamics of statistical data on water withdrawal from natural water reservoirs for practical use, as well as on discharge of polluted sewage, and also differentiated the data obtained by the main types of economic activity (industries). Some conclusions are made on the effectiveness of the implementation of measures for the protection of water resources for each type of activity. The article highlights the industries using water resources most efficiently over the past 10 years and systematically implementing measures to reduce the discharge of polluted wastewater into surface water bodies. The study shows in which industries the efficiency of water purification and water use activities has decreased for the same period. The results of the analysis can be used to optimize and manage measures for the use and conservation of water resources for certain types of economic activities.
Monitoring research and care for nature technologies in biosphere reserves UNESCO
Authors: Roshchevskiy Yu K , Vekhnik V A
Published: July 2021

In biosphere reserves UNESCO, we propose to distinguish scientific research studying the unknown qualities of the biota from technological design aimed at restoring and caring for the ecosystems of a reserve. In primary or climax ecosystems, we propose to use technological methods that prevent anthropogenic transformation. In secondary and degraded ecosystems at different levels, we propose artificial restoring of the lost functions of ecosystems. Examples of monitoring studies in ecosystems with varying degrees of disturbance in the Middle-Volga Integrated Biosphere Reserve are considered.
Effect of cadmium on the mesophyll parameters, pigments, and lipid profile of the photosynthetic apparatus of Suaeda salsa
Authors: Rozentsvet O A
Published: July 2021

Halophytes were found to accumulate HM ions in their tissues; therefore, they are potentially useful for remediation of soil contaminated by salt or HM. In this study, we evaluated the effect of Cd2+ on the characteristics of mesophyll, pigments, and lipid profile of the photosynthetic organelles of the halophyte Suaeda salsa. Seeds were sprouted in distilled water for 1–3 days and then sown in containers with sand. Plants were watered with Robinson’s nutrient solution. After 3 months, plants were divided into two groups: experimental and control. In the experimental group, soil was treated with 200 µM Cd(NO3)2 for 24 hours. Our findings suggest that Cd2+ causes changes in the anatomical structure of the leaf and the ultrastructure of the photosynthetic organelles in S. salsa due to alterations in the composition of lipids and fatty acids.
Interannual and intra-annual changes in the Volga River water discharge in the alignment of the Zhigulevsk hydroelectric complex
Authors: Seleznev V A
Published: July 2021

Interannual and intra-annual changes in river water flow play a decisive role in the formation of water quality and the functioning of aquatic ecosystems. For a quantitative assessment of long-term and seasonal changes in the water flow of the Volga River, an analysis of water discharge in the outlet section of the Kuibyshev reservoir (Zhigulevsky hydroelectric complex) for the period 1958-2019 was carried out. Almost the entire water flow of the Volga River passes through the bottom spillways of the hydroelectric power station and the overflow dam of the Zhigulevsky hydroelectric complex. The results of time series analysis showed that the average annual water discharge was 7,7 × 103 m3/s, the highest water discharge was 10,4 × 103 m3/s, and the lowest water discharge was 5,3 × 103 m3/s. Over a long-term observation period (61 years), it was established that the water content of the river is characterized by a change in low water and high-water periods. Statistical analysis revealed a positive trend for an increase in the average annual water discharge of the Volga River by 700 m3/s. Extremely low-water (1996, 1977, 1976, 1975, 1973, 1967) and extremely high-water (1994, 1991, 1990, 1981, 1979, 1966) years have been identified. The regulation of water flow at the Zhigulevsky hydroelectric complex has formed the seasonal variability of water discharge, which is characteristic of technical water bodies. Within the year, three periods are distinguished: winter low-water period (December-March), spring high water (April-June), and summer-autumn low-water period (July-November). The highest water discharges were observed during the spring flood (8,7-19,6 × 103 m3/s). During the winter and summer-autumn low-water period, the water discharge was 5,5-6,5 × 103 m3/s. The amplitude of fluctuations in the average monthly water discharge for the entire observation period was 2,1-33,5 × 103 m3/s.
Accessibility of protected natural areas of regional significance: a case study from Samara Oblast, Russia
Authors: Sidorov A A , Kudinova G E , Kostina N V
Published: July 2021

A significant role is assigned to the preservation of natural areas in the paradigm of sustainable development both in the international and regional aspects. Protected natural areas of regional importance make it possible to solve the problem of the preservation of natural ecosystems. The aim of the research is to establish for the municipal districts of Samara Oblast: dynamics, formation features and provision of PAs of regional significance. In the course of the study, on the basis of analysis, logical presentation, and statistical research, the authors established: the dynamics, features of the formation and provision of the municipal districts of Samara Oblast with specially protected natural areas of regional significance. The authors show a significant variability in areas, specific value and provision of the local population with specially protected natural areas, the relationship of individual parameters. The authors also built a rating and compiled a classification of municipal districts according to the given indicators. The authors identified the categories of municipal districts with a high, medium and low share of specially protected natural areas in the total area of the subregional area and the provision of the population with protected areas. The authors studied various options or models of compensatory benefits and environmental costs of municipal areas, taking into account specially protected natural areas of federal significance and the influence of the urban environment. The results of the analysis make it possible to use the obtained materials for making current managerial decisions in the interaction of regional environmental authorities with the administrations of municipal districts, for correcting the prospective scheme for the development of specially protected natural areas of regional significance, and for modernizing the development strategies of territories.
Program-targeted land reclamation In Samara Oblast (Russia)
Authors: Sidorov A A , Kudinova G E , Kostina N V , Kudinov A K
Published: July 2021

In the article, the authors consider the current state and a number of measures aimed at solving the problems of land reclamation of agricultural lands in Samara Oblast. A feature of the implementation of the land reclamation program on a regional scale is the use of the program-targeted method and issues of state stimulation of its development, as well as the possibility of attracting extrabudgetary funds for the implementation of investment projects. Such a program is ultimately aimed at increasing the volume of crop and livestock production, as well as preserving existing and creating new jobs. In the article, the authors assess the objectives, tactical indicators, resource support and the course of implementation of state programs for land reclamation support in Samara Oblast. The authors note that during the study period in Samara Region, modernization of existing reclamation systems was carried out, new irrigation systems were built, and previously abandoned agricultural land was restored. As part of targeted funding, the state provides grants for the development of design estimates for the implementation of investment projects in the field of land reclamation. The authors believe that, in general, the progress of the implementation of the state program of land reclamation should be considered very effective.
Macrozoobenthos communities in the Kuybyshev reservoir Priplotinnyi Reach: long-term dynamics
Authors: Zinchenko T D , Abrosimova E V , Golovatyuk L V
Published: July 2021

The authors analyzed the dynamics of benthic communities in the Kuybyshev Reservoir Priplotinnyi Reach, over a long-term observation period 1958-2020. The authors note a certain frequency of changes in the ratio of macrozoobenthos coenoses and biomass of benthic communities at the stations of the former Volga channel and the Priplotinnyi Reach floodplain. During the research period in 2005, 2020 there was a decrease in the biomass of benthos. The stage of destabilization of the Kuybyshev reservoir ecosystem, noted since the mid-1980s, against the background of anthropogenic eutrophication processes, is accompanied by a sharp decrease in the biomass of benthos and structural changes in benthic communities. In 2020, the benthos biomass, compared to 1985, decreased in deep-water areas and in the Priplotinnyi Reach coastal zone by about 8 times and amounted to 2.0 g / m2, which is due to a decrease in the proportion of pelophilic coenosis of oligochaetes Tubifex tubife and Limnodrilus hoffmeisteri. The biomass of forage benthos in the coastal zone decreased from 5.48 g / m2 to 2.94-1.75 g / m2 due to anthropogenic impact. The authors revealed similar processes of development of the chironomid coenosis on the former channel and the flooded floodplain. During the autumn survey, 9 species were recorded in shallow waters, the proportion of which is 19.5%. There was found a low biomass of Procladius ferrugineus larvae -0.05 -0.08 g / m2. The authors discuss the data of hydrobiological monitoring at the stations of the former channel and the flooded floodplain of the Priplotinnyi Reach, including the change in the coenosis of chironomids (Diptera, Chironomidae) as an object of indication of the ecological state of the reservoir.
Frugal discrete memristive device based on potassium permanganate solution
Authors: Revadekar Chetan C , Takaloo Ashkan Vakilipour , Shinde Sandeep P , Patil Swapnil R , Kundale Somnath S , Kim Deok-kee , Dongale Tukaram D
Published: July 2021

Many thin film-based devices with solid electrolytes have been studied for memristive applications. Herein, we report a simple and facile way to fabricate solution-based, low-cost, and discrete two-terminal memristive devices using the KMnO4 solution. The water and methanol were used as a solvent to prepare different concentrations of KMnO4 to carry out the optimization study. Furthermore, the effect of KMnO4 concentration with aqueous and methanol solvents was studied with the help of current-voltage, device charge, charge-flux, and cyclic endurance properties. Interestingly, all developed devices show the asymmetric time-domain charge and double valued charge-flux properties, suggesting that aqueous KMnO4 and methanol-KMnO4 based devices are non-ideal memristors or memristive devices. The statistical measures such as cumulative probability and coefficient of variation are reported for the memristive devices. The possible switching mechanism of the discrete memristive was tried to explain with the UV-visible spectrum and theoretical framework. The optimized device was further studied using the cyclic voltammogram, Bode plot, and Nyquist plot. An equivalent circuit was derived for the optimized discrete memristive device using electrochemical impendence spectroscopy results. The results of the present investigation are beneficial to develop programmable analog circuits, volatile memory, and synaptic devices using discrete memristive devices.
Depinning behavior of the vortex domain wall at the asymmetric triangular notch in permalloy wires
Authors: Shiu Deng-Shiang , Lai Kao-Fan , Liu Yi-Ying , Li Yuan-Ting , Gao Zhi-En , Kao Yee-Mou , Wu Jong-Ching , Horng Lance
Published: July 2021

The depinning field (H
D) of vortex domain walls in a permalloy wire with an asymmetric triangle notch was investigated through magneto-optic Kerr effect (MOKE) microscopy and micromagnetic simulations. Wires of various widths with notches fixed on the wall’s incoming side angle were studied for various outgoing side angles (ϕ). The curves of H
D of wall versus ϕ were measured by MOKE microscopy. Micromagnetic simulations were used to obtain curves of the H
D of the wall versus ϕ. The maximum of such a curve of tail-to-tail -clockwise wall is known as the transition angle (ϕ
T). The shape-anisotropic energy (E
A) of the notch outgoing side wire and the exchange energy (E
Ex) of the wall–notch interaction competed to influence the ϕ
T value. Pinning potential was increased by the E
Ex when ϕ was smaller than the ϕ
T. Pinning potential was considerably reduced by the small E
A when ϕ was larger than the ϕ
T. Furthermore, the ϕ
T value changed with the decrease in the depth of the notch because E
A was influenced by notch depth.
Change of Practice Patterns Following an Educational Comment on Reports of Benign-Appearing Endometrial Cells in Papanicolaou Tests
Authors: Jones Terri E , Onisko Agnieszka , Austin R Marshall , Yu Jing
Published: July 2021

Objectives

Since the publication of our study demonstrating high negative predictive values (>99% for women in their 40s) of benign-appearing endometrial cells (nEMCs), we have begun to include an educational comment in Papanicolaou (Pap) test reports with nEMCs that recommends routine periodic screening for asymptomatic premenopausal women (APW). The current study evaluated how the inclusion of this comment has affected clinical practice patterns at our institution.

Methods

The 2017 to 2019 database identified 175 reports containing the educational comment in women aged 45 to 54 years with a follow-up time of 11 to 37 months. Data, including age, menopause status, symptoms, imaging, and outcome, were collected. The procedure rate and the impact of clinical modifiers were assessed.

Results

Thirty-seven (20.6%) patients had biopsies within 6 months, which decreased from 48.1% as we previously reported. All nine (5%) APW with biopsies triggered only by nEMCs had benign histopathology. The remaining 28 biopsied patients had abnormal bleeding or a thickened endometrium, or they were postmenopausal, including a 53-year-old patient with complex atypical hyperplasia. None of the 138 patients with conservative follow-up developed atypical/malignant lesions.

Conclusions

A qualifying educational note included in Pap reports significantly reduced follow-up biopsies in APW. Optimal follow-up of nEMCs should be based on relevant clinical modifiers.
Role of Age in the Spread of Influenza, 2011–2019: Data From the US Influenza Vaccine Effectiveness Network
Authors: Griggs Eric P , Flannery Brendan , Foppa Ivo M , Gaglani Manjusha , Murthy Kempapura , Jackson Michael L , Jackson Lisa A , Belongia Edward A , McLean Huong Q , Martin Emily T , Monto Arnold S , Zimmerman Richard K , Balasubramani Goundappa K , Chung Jessie R , Patel Manish ,   for the US Influenza Vaccine Effectiveness Study Investigators
Published: July 2021

Intraseason timing of influenza infection among persons of different ages could reflect relative contributions to propagation of seasonal epidemics and has not been examined among ambulatory patients. Using data from the US Influenza Vaccine Effectiveness Network, we calculated risk ratios derived from comparing weekly numbers of influenza cases prepeak with those postpeak during the 2010–2011 through 2018–2019 influenza seasons. We sought to determine age-specific differences during the ascent versus descent of an influenza season by influenza virus type and subtype. We estimated 95% credible intervals around the risk ratios using Bayesian joint posterior sampling of weekly cases. Our population consisted of ambulatory patients with laboratory-confirmed influenza who enrolled in an influenza vaccine effectiveness study at 5 US sites during 9 influenza seasons after the 2009 influenza A virus subtype H1N1 (H1N1) pandemic. We observed that young children aged <5 years tended to more often be infected with H1N1 during the prepeak period, while adults aged ≥65 years tended to more often be infected with H1N1 during the postpeak period. However, for influenza A virus subtype H3N2, children aged <5 years were more often infected during the postpeak period. These results may reflect a contribution of different age groups to seasonal spread, which may differ by influenza virus type and subtype.
Lifestyle Behaviors Among Adults Recommended for Ambulatory Blood Pressure Monitoring According to the 2017 ACC/AHA Blood Pressure Guideline
Authors: Cohen Laura P , Hubbard Demetria , Colvin Calvin L , Jaeger Byron C , Poudel Bharat , Abdalla Marwah , Langford Aisha T , Hardy Shakia T , Sims Mario , Lewis Cora E , Muntner Paul , Shimbo Daichi
Published: July 2021

Background

The 2017 American College of Cardiology/American Heart Association blood pressure (BP) guideline recommends ambulatory BP monitoring to exclude white coat hypertension (WCH) among adults with office systolic BP (SBP)/diastolic BP (DBP) of 130–159/80–99 mm Hg, and masked hypertension (MHT) among adults with office SBP/DBP of 120–129/75–79 mm Hg after a 3-month trial of lifestyle modification. We estimated the proportion of individuals with ideal lifestyle factors among those who meet these office BP criteria.

Methods

We analyzed data from participants not taking antihypertensive medication in the Coronary Artery Risk Development in Young Adults (CARDIA) and Jackson Heart Study (JHS) who met the office BP criteria for screening for WCH (CARDIA n = 490, JHS n = 873) and MHT (CARDIA n = 486, JHS n = 614). We estimated the prevalence of lifestyle factors including ideal body mass index (BMI), physical activity, diet, and alcohol use among participants who met office BP criteria for WCH or MHT screening.

Results

Among participants who met office BP criteria for WCH screening, 15.5% in CARDIA and 3.6% in JHS had 3 or more ideal lifestyle factors. Among participants who met office BP criteria for MHT screening, 22.6% in CARDIA and 4.7% in JHS had 3 or more ideal lifestyle factors. Ideal BMI, diet, and physical activity were present in less than half of participants in each sample.

Conclusions

Few participants who met office BP criteria for the screening of WCH or MHT had ideal lifestyle factors.
Machine learning approaches for drug combination therapies
Authors: Güvenç Paltun Betül , Kaski Samuel , Mamitsuka Hiroshi
Published: July 2021

Drug combination therapy is a promising strategy to treat complex diseases such as cancer and infectious diseases. However, current knowledge of drug combination therapies, especially in cancer patients, is limited because of adverse drug effects, toxicity and cell line heterogeneity. Screening new drug combinations requires substantial efforts since considering all possible combinations between drugs is infeasible and expensive. Therefore, building computational approaches, particularly machine learning methods, could provide an effective strategy to overcome drug resistance and improve therapeutic efficacy. In this review, we group the state-of-the-art machine learning approaches to analyze personalized drug combination therapies into three categories and discuss each method in each category. We also present a short description of relevant databases used as a benchmark in drug combination therapies and provide a list of well-known, publicly available interactive data analysis portals. We highlight the importance of data integration on the identification of drug combinations. Finally, we address the advantages of combining multiple data sources on drug combination analysis by showing an experimental comparison.
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints
Authors: Won Dhong-Gun , Kim Dong-Wook , Woo Junwoo , Lee Kyoungyeul
Published: July 2021

Motivation

Improvements in next-generation sequencing have enabled genome-based diagnosis for patients with genetic diseases. However, accurate interpretation of human variants requires knowledge from a number of clinical cases. In addition, manual analysis of each variant detected in a patient's genome requires enormous time and effort. To reduce the cost of diagnosis, various computational tools have been developed to predict the pathogenicity of human variants, but the shortage and bias of available clinical data can lead to overfitting of algorithms.

Results

We developed a pathogenicity predictor, 3Cnet, that uses recurrent neural networks to analyze the amino acid context of human variants. As 3Cnet is trained on simulated variants reflecting evolutionary conservation and clinical data, it can find disease-causing variants in patient genomes with 2.2 times greater sensitivity than currently available tools, more effectively discovering pathogenic variants and thereby improving diagnosis rates.

Availability and implementation

Codes (https://github.com/KyoungYeulLee/3Cnet/) and data (https://zenodo.org/record/4716879#.YIO-xqkzZH1) are freely available to non-commercial users.

Supplementary information

Supplementary data are available at Bioinformatics online.
HeterozygousHTRA1nonsense or frameshift mutations are pathogenic
Authors: Coste Thibault , Hervé Dominique , Neau Jean Philippe , Jouvent Eric , Ba Fatoumata , Bergametti Françoise , Lamy Matthias , Cogez Julien , Derache Nathalie , Schneckenburger Romain , Grelet Maude , Gollion Cédric , Lanotte Livia , Lauer Valérie , Layet Valérie , Urbanczyk Cédric , Didic Mira , Raynouard Igor , Delaval Laure , Dassa Jérémie , Florea Alexandru , Badiu Carmen , Nguyen Karine , Tournier-Lasserve Elisabeth
Published: July 2021

Heterozygous missense HTRA1 mutations have been associated with an autosomal dominant cerebral small vessel disease (CSVD) whereas the pathogenicity of heterozygous HTRA1 stop codon variants is unclear. We performed a targeted high throughput sequencing of all known CSVD genes, including HTRA1, in 3853 unrelated consecutive CSVD patients referred for molecular diagnosis. The frequency of heterozygous HTRA1 mutations leading to a premature stop codon in this patient cohort was compared with their frequency in large control databases. An analysis of HTRA1 mRNA was performed in several stop codon carrier patients. Clinical and neuroimaging features were characterized in all probands. Twenty unrelated patients carrying a heterozygous HTRA1 variant leading to a premature stop codon were identified. A highly significant difference was observed when comparing our patient cohort with control databases: gnomAD v3.1.1 [P = 3.12 × 10−17, odds ratio (OR) = 21.9], TOPMed freeze 5 (P = 7.6 × 10−18, OR = 27.1) and 1000 Genomes (P = 1.5 × 10−5). Messenger RNA analysis performed in eight patients showed a degradation of the mutated allele strongly suggesting a haploinsufficiency. Clinical and neuroimaging features are similar to those previously reported in heterozygous missense mutation carriers, except for penetrance, which seems lower. Altogether, our findings strongly suggest that heterozygous HTRA1 stop codons are pathogenic through a haploinsufficiency mechanism. Future work will help to estimate their penetrance, an important information for genetic counselling.
Nicotine promotes vascular calcification via intracellular Ca2+-mediated, Nox5-induced oxidative stress, and extracellular vesicle release in vascular smooth muscle cells
Authors: Petsophonsakul Ploingarm , Burgmaier Mathias , Willems Brecht , Heeneman Sylvia , Stadler Nadina , Gremse Felix , Reith Sebastian , Burgmaier Kathrin , Kahles Florian , Marx Nikolaus , Natour Ehsan , Bidar Elham , Jacobs Michael , Mees Barend , Reutelingsperger Chris , Furmanik Malgorzata , Schurgers Leon
Published: July 2021

Aims

Smokers are at increased risk of cardiovascular events. However, the exact mechanisms through which smoking influences cardiovascular disease resulting in accelerated atherosclerosis and vascular calcification are unknown. The aim of this study was to investigate effects of nicotine on initiation of vascular smooth muscle cell (VSMC) calcification and to elucidate underlying mechanisms.

Methods and results

We assessed vascular calcification of 62 carotid lesions of both smoking and non-smoking patients using ex vivo micro-computed tomography (µCT) scanning. Calcification was present more often in carotid plaques of smokers (n = 22 of 30, 73.3%) compared to non-smokers (n = 11 of 32, 34.3%; P < 0.001), confirming higher atherosclerotic burden. The difference was particularly profound for microcalcifications, which was 17-fold higher in smokers compared to non-smokers. In vitro, nicotine-induced human primary VSMC calcification, and increased osteogenic gene expression (Runx2, Osx, BSP, and OPN) and extracellular vesicle (EV) secretion. The pro-calcifying effects of nicotine were mediated by Ca2+-dependent Nox5. SiRNA knock-down of Nox5 inhibited nicotine-induced EV release and calcification. Moreover, pre-treatment of hVSMCs with vitamin K2 ameliorated nicotine-induced intracellular oxidative stress, EV secretion, and calcification. Using nicotinic acetylcholine receptor (nAChR) blockers α-bungarotoxin and hexamethonium bromide, we found that the effects of nicotine on intracellular Ca2+ and oxidative stress were mediated by α7 and α3 nAChR. Finally, we showed that Nox5 expression was higher in carotid arteries of smokers and correlated with calcification levels in these vessels.

Conclusion

In this study, we provide evidence that nicotine induces Nox5-mediated pro-calcific processes as novel mechanism of increased atherosclerotic calcification. We identified that activation of α7 and α3 nAChR by nicotine increases intracellular Ca2+ and initiates calcification of hVSMCs through increased Nox5 activity, leading to oxidative stress-mediated EV release. Identifying the role of Nox5-induced oxidative stress opens novel avenues for diagnosis and treatment of smoking-induced cardiovascular disease.
Evaluation of 13-Tetradecenyl Acetate Pheromone for Melanotus communis (Coleoptera: Elateridae) Detection in North Carolina Row Crop Agroecosystems
Authors: Pellegrino Alyssa M , Dorman Seth J , Williams Livy , Millar Jocelyn G , Huseth Anders S
Published: July 2021

Melanotus communis Gyllenhal (Coleoptera: Elateridae) larvae are a common soil-dwelling pest of many crops, including sweet potato, grains, and tobacco. Although many studies have focused on the larval stage of this pest, the seasonal activity and ecology of the adults (click beetles) are not well understood. The overarching goal of this study was to relate M. communis adult activity to host crops in the North Carolina row-crop agroecosystem. To do this, we conducted a two-year study documenting male M. communis activity, using a recently identified sex attractant pheromone, 13-tetradecenyl acetate. This project was divided into two parts: 1) a pheromone assessment study testing the efficacy and specificity of 13-tetradecenyl acetate, and two analogs, 13-tetradecenyl butyrate and 13-tetradecenyl hexanoate, and 2) a landscape survey using traps baited with 13-tetradecenyl acetate. Results of the efficacy study showed that 13-tetradecenyl acetate was the most effective M. communis lure when compared to non-baited control traps or traps baited with the two homologs. The landscape study documented a strong association between M. communis catch and the adjacent crop type. We found that adult M. communis abundance was greatest near corn, followed by sweet potato, and then cotton. Analysis of activity over time found that the peak activity occurred during July. Overall, this project demonstrates the usefulness of pheromone-baited traps in providing new information about M. communis activity.
Persistence and spread of tetracycline resistance genes and microbial community variations in the soil of animal corrals in a semi-arid planted forest
Authors: Nejidat Ali , Diaz-Reck Damiana , Gelfand Ilya , Zaady Eli
Published: July 2021

At the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1–10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23–26%) than in the other corrals and the control (33–38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1–10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.
Genomic prediction in family bulks using different traits and cross-validations in pine
Authors: Rios Esteban F , Andrade Mario H M L , Resende Marcio F R , Kirst Matias , de Resende Marcos D V , de Almeida Filho Janeo E , Gezan Salvador A , Munoz Patricio
Published: July 2021

Genomic prediction integrates statistical, genomic, and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in mating systems, breeding schemes, propagation methods, and unit of selection, no universal genomic prediction approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5–20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values (GEBV) at the individual and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of genomic prediction in these situations.
Phylogenomics of Opsin Genes in Diptera Reveals Lineage-Specific Events and Contrasting Evolutionary Dynamics in Anopheles and Drosophila
Authors: Feuda Roberto , Goulty Matthew , Zadra Nicola , Gasparetti Tiziana , Rosato Ezio , Pisani Davide , Rizzoli Annapaola , Segata Nicola , Ometto Lino , Stabelli Omar Rota
Published: July 2021

Diptera is one of the biggest insect orders and displays a large diversity of visual adaptations. Similarly to other animals, the dipteran visual process is mediated by opsin genes. Although the diversity and function of these genes are well studied in key model species, a comprehensive comparative genomic study across the dipteran phylogeny is missing. Here we mined the genomes of 61 dipteran species, reconstructed the evolutionary affinities of 528 opsin genes, and determined the selective pressure acting in different species. We found that opsins underwent several lineage-specific events, including an independent expansion of Long Wave Sensitive opsins in flies and mosquitoes, and numerous family-specific duplications and losses. Both the Drosophila and the Anopheles complement are derived in comparison with the ancestral dipteran state. Molecular evolutionary studies suggest that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher in Anopheles than in Drosophila. Overall, our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations, Anopheles and Drosophila, are characterized by contrasting dynamics in the evolution of this gene family. These results provide a foundation for future studies on the dipteran visual system.
The Transcriptional Regulator Hap1p (Cyp1p) Is Essential for Anaerobic or Heme-Deficient Growth of Saccharomyces cerevisiae: Genetic and Molecular Characterization of an Extragenic Suppressor that Encodes a WD Repeat Protein
Authors: Chantrel Yann , Gaisne Mauricette , Lions Claire , Verdière Jacqueline
Published: July 2021

We report here that Hap1p (originally named Cyp1p) has an essential function in anaerobic or heme-deficient growth. Analysis of intragenic revertants shows that this function depends on the amino acid preceding the first cysteine residue of the DNA-binding domain of Hap1p. Selection of recessive extragenic suppressors of a hap1−hem1− strain allowed the identification, cloning, and molecular analysis of ASC1 (Cyp1 Absence of growth Supressor). The sequence of ASC1 reveals that its ORF is interrupted by an intron that shelters the U24 snoRNA. Deletion of the intron, inactivation of the ORF, and molecular localization of the mutations show unambiguously that it is the protein and not the snoRNA that is involved in the suppressor phenotype. ASC1, which is constitutively transcribed, encodes an abundant, cytoplasmically localized 35-kD protein that belongs to the WD repeat family, which is found in a large variety of eucaryotic organisms. Polysome profile analysis supports the involvement of this protein in translation. We propose that the absence of functional Asc1p allows the growth of hap1−hem1− cells by reducing the efficiency of translation. Based on sequence comparisons, we discuss the possibility that the protein intervenes in a kinase-dependent signal transduction pathway involved in this last function.
Dhh1p, a Putative RNA Helicase, Associates with the General Transcription Factors Pop2p and Ccr4p from Saccharomyces cerevisiae
Authors: Hata Hiroaki , Mitsui Hisayuki , Liu Hong , Bai Yongli , Denis Clyde L , Shimizu Yuki , Sakai Akira
Published: July 2021

The POP2 (Caf1) protein in Saccharomyces cerevisiae affects a variety of transcriptional processes and is a component of the Ccr4p complex. We have isolated five multicopy suppressor genes of a pop2 deletion mutation: CCR4, DHH1 (a putative RNA helicase), PKC1, STM1, and MPT5 (multicopy suppressor of pop two). Overexpression of either the CCR4 or DHH1 genes effectively suppressed phenotypes associated with pop2 mutant cells; overexpression of PKC1, STM1, or MPT5 genes produced only partial suppression. Disruption of the CCR4 or DHH1 genes resulted in phenotypes similar to those observed for pop2 cells. In addition, overexpression of the DHH1 gene also suppressed the ccr4 mutation, suggesting a close relationship between the POP2, CCR4, and DHH1 genes. Two-hybrid analysis and coimmunoprecipitation experiments revealed that Pop2p and Dhh1p interact physically, and these and other data suggest that Dhh1p is also a component of the Ccr4p complex. Finally, we investigated the genetic interaction between factors associated with POP2 and the PKC1 pathway. The temperature-sensitive growth defect of dhh1 or mpt5 cells was suppressed by overexpression of PKC1, and the defect of mpk1 cells was suppressed by overexpression of MPT5. These results and phenotypic analysis of double mutants from the POP2 and PKC1 pathways suggested that the POP2 and the PKC1 pathways are independent but have some overlapping functions.
Yeast Meiotic Mutants Proficient for the Induction of Ectopic Recombination
Authors: Engebrecht JoAnne , Masse Sherie , Davis Luther , Rose Kristine , Kessel Therese
Published: July 2021

A screen was designed to identify Saccharomyces cerevisiae mutants that were defective in meiosis yet proficient for meiotic ectopic recombination in the return-to-growth protocol. Seven mutants alleles were isolated; two are important for chromosome synapsis (RED1, MEK1) and five function independently of recombination (SPO14, GSG1, SPOT8/MUM2, 3, 4). Similar to the spoT8-1 mutant, mum2 deletion strains do not undergo premeiotic DNA synthesis, arrest prior to the first meiotic division and fail to sporulate. Surprisingly, although DNA replication does not occur, mum2 mutants are induced for high levels of ectopic recombination. gsg1 diploids are reduced in their ability to complete premeiotic DNA synthesis and the meiotic divisions, and a small percentage of cells produce spores. mum3 mutants sporulate poorly and the spores produced are inviable. Finally, mum4-1 mutants produce inviable spores. The meiotic/sporulation defects of gsg1, mum2, and mum3 are not relieved by spo11 or spo13 mutations, indicating that the mutant defects are not dependent on the initiation of recombination or completion of both meiotic divisions. In contrast, the spore inviability of the mum4-1 mutant is rescued by the spo13 mutation. The mum4-1 spo13 mutant undergoes a single, predominantly equational division, suggesting that MUM4 functions at or prior to the first meiotic division. Although recombination is variably affected in the gsg1 and mum mutants, we hypothesize that these mutants define genes important for aspects of meiosis not directly related to recombination.
Dominant Alleles of Saccharomyces cerevisiae CDC20 Reveal Its Role in Promoting Anaphase
Authors: Schott Eric J , Hoyt M Andrew
Published: July 2021

We identified an allele of Saccharomyces cerevisiae CDC20 that exhibits a spindle-assembly checkpoint defect. Previous studies indicated that loss of CDC20 function caused cell cycle arrest prior to the onset of anaphase. In contrast, CDC20-50 caused inappropriate cell cycle progression through M phase in the absence of mitotic spindle function. This effect of CDC20-50 was dominant over wild type and was eliminated by a second mutation causing loss of function, suggesting that it encodes an overactive form of Cdc20p. Overexpression of CDC20 was found to cause a similar checkpoint defect, causing bypass of the preanaphase arrest produced by either microtubule-depolymerizing compounds or MPS1 overexpression. CDC20 overexpression was also able to overcome the anaphase delay caused by high levels of the anaphase inhibitor Pds1p, but not a mutant form immune to anaphase-promoting complex- (APC-)mediated proteolysis. CDC20 overexpression was unable to promote anaphase in cells deficient in APC function. These findings suggest that Cdc20p is a limiting factor that promotes anaphase entry by antagonizing Pds1p. Cdc20p may promote the APC-dependent proteolytic degradation of Pds1p and other factors that act to inhibit cell cycle progression through mitosis.