bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Nitrogen Fertilizer and Rate of Seeds on Some Growth Criteria and Dry Matter Production of Barley (Hordeum Vulgare L.)
Authors: Rahi AL-HamdawiEsra , Mihbis AL-Tahir Faisal
Published: November 2021

A field experiment was carried out at the Second Agricultural Research and Experiments Station of the College of Agriculture/University of Al-Muthanna in Al Bandar region, during the winter season (2019-2020), in order to know the effect of nitrogen fertilization and seed rate on the production of dry matter for barley crop, and the experiment was applied according to the arrangement of the split plates. According to the design of randomized complete blocks with three replications, the number of experimental units was 120 units. The experiment included the secondary factor of five seed quantities (40, 60, 80, 100 and 120 kg ha−1) and the main factor included 4 levels of nitrogen fertilizer (0, 50, 100 and 150 kg ha−1). The results showed that the rate of seed were significantly superior in most of the growth characteristics and dry matter of the barley crop, where the rate of seeds 80 kg ha-1 outperformed in the characteristics of plant height, dry weight of the stem, dry weight of leaves, dry weight of ears and dry weight of the plant, where their averages were (96.64 cm, 10.34 g, 7.20 g, 4.78 g and 22.3 g) respectively, while the level of 120 kg ha−1 seed rate outperformed in increasing the area of the flag leaf, which amounted to 23.67 cm 2, and the lowest seed level 40 kg ha-1 gave an increase in the length of the spike, which reached 7.06 cm. As for nitrogen fertilizer levels, the levels were significantly higher in all studied traits, where the amount of fertilizer 100 kg ha−1 outperformed in all studied traits, plant height (100.20 cm) and area leaf flag (24.38 cm 2), the number of tillers (8.38 tillers Plant−1, the length of the spike (6.92 cm), the dry weight of the stem (10.84 g), the leaves (7.29 g), the spikes (5.38 g), and the dry weight of the whole plant (23.51 g). As for the interaction between the rate of seed and nitrogen fertilization, the combination (80 kg ha−1 seed * 100 kg ha−1 nitrogen) outperformed and gave the highest averages for most of the studied traits. And the weight of the full bat where their averages were (13.20, 10.51, 7.37 and 31.07 g) respectively.
Effect Irrigation Quality and Mineral Fertilization on Barley Productivity (Variety 244) and Some Nutrients Availability
Authors: Al-Maamori Haider.A. , Al-Budeiri Montazer.H. , Mousa Raji A.
Published: November 2021

An experiment was conducted in fields of Agricultural Research office/Al-Dibuni Research Station in Clay Loam soil, to study the coexistence with irrigation salinity using different water qualities with a recommended mineral fertilizer by the Iraqi Ministry of Agriculture, and evaluate the role of this fertilizer in maintaining the nutritional balance in soil and barley productivity. A Factorial Experiment Design was used According to RCBD design. The results showed that mineral fertilization of 100% fertilizer recommendation was significantly superior in all measured characteristics (nitrogen and phosphorus availability in soil, EC, plant height, leaf area, number of branches, 1000 grain weight, grain yield, biological yield and harvest index) which gave (46.31, 27.29 mg kg−1, 5.59 dSm−1, 67.44 cm, 20.41 cm2plant−1, 7.66 branch plant−1, 44.08g, 3.16, 11.19 Mg ha−1, and 28.24%, respectively) compared with control treatment. The addition of irrigation different types affected on the measured characteristics, as the S1 treatment gave a significant values in each of (nitrogen and phosphorus availability in soil, EC, leaf area, number of branches, 1000 grain weight, grain yield, biological yield and harvest index) which gave (40.27, 23.39 mg kg−1, 5.10 dSm−1, 16.97 cm2plant−1, 6.91 branch plant−1, 40.31 g, 3.02, 10.13 Mgha−1, and 29.98%) compared with S2 treatment. The results showed the double interaction F4S3 treatment had a significant effect in all the measured characteristics(nitrogen and phosphorus availability in soil, leaf area, number of branches, 1000 grain weight, grain yield, biological yield and harvest index) which gave (48.61 and 28.97mg kg−1 and 20. 92 cm2plant−1, 8.06 branch plant−1, 45.75g, 3.22, 11.47 Mgha−1, and 28.07%, respectively) compared with F1S2 treatment, noting F4S3 treatment did not significantly of F4S1 treatment.
The Effect of Chelated Zinc and Nano-Zinc and Interaction on Growth Traits of Wheat (Triticum Aestivum L.)
Authors: Mohammed Al-Toki Mohammed Abed , Halloul Rahim
Published: November 2021

The field experiment was carried out in one of the farmers’ fields in Al-Fajr district, Dhi Qar governorate, located 90 km north of Nasiriyah city center, during the agricultural season 2020-2021. To show the effect of spraying different levels of chelated and nano zinc on the growth of wheat (Triticum aestivum L.). The experiment was conducted using factorial experiments according to the complete block design (RCBD). The experiment included two factors, the first factor using chelated zinc at five levels (0, 40, 80, 120 and 160 mg. L−1), and the second factor using nano-zinc at five levels (0, 40, 80, 120 and 160 mg. L−1). The results show that chelated zinc was a significant effect on the leaf area, the flag leaf, tiller number and chlorophyll, and no significant effect on plant height and spike length. As for the zinc nanoparticles, it had a significant effect on leaf area and chlorophyll, and no significant effect on the plant height, spike length and the tiller number. While the interaction affected significantly the leaf area, and no significantly affect the plant height, spike length, tiller number and chlorophyll.
Effect of Sulfur-Oxidizing Bacteria Thiobacillus Thioparus and Different Levels of Agricultural Sulfur on Wheat Yield (Triticum Aestivium L.)
Authors: Jabbar Abdullah Karim , Al-Ziyadi Dalia Qassem
Published: November 2021

A field experiment was carried out in the agricultural season 2020-2021 in an agricultural field located in the Al-Jarboua area (Al Hafez) in Al-Muthanna Governorate to study the effect of inoculation with sulfur-oxidizing bacteria and agricultural sulfur levels and their interactions on the yield of wheat plant Triticum aestivum L. Ibaa cultivar 99. The study was carried out in two stages, the first is isolation Sulfur oxidizing bacteria and the second used as a inoculant in the agricultural experiment to study its effect on soil characteristics and its content of nutrients NPK and S. At two levels T0 without adding the bacterial inoculum and T1 adding the first isolate of bacteria The second factor included the addition of agricultural sulfur with four levels of sulfur (S0 were taken without addition, S1 added 750 kg ha−1, S2 added 1500 kg ha−1 and S3 added 2250 kg ha−1) In three replications, the number of experimental units reached 36 experimental units. The results of the study also showed that inoculation with bacterial isolates led to a significant increase in the readiness of nutrients N, P, K and S, and the highest rate of sulfur was (1895) mg. The pollination also led to a significant increase in the growth characteristics of the plant (plant height, number of spikes and grain yield), as it recorded (101.25 cm, 393.22 spike m−1 and 6.73 mcg/ha−1), respectively. The addition of agricultural sulfur at different levels affected a significant increase in the availability of nutrients N, P, K and S, and the highest rate of sulfur at the level of S3 was (1817) mg. Also, the bilateral interaction between inoculation with bacterial isolates and agricultural sulfur led to a significant increase in the availability of nutrients N, P, K and S. kg −1 soil.
The Effect of Type and Method of Immobilizing Bacillus Megaterium Bacteria Inoculation in Increasing Potassium Available and Growth of Wheat Plant Triticum Aestivum L
Authors: Al-Jubouri Abdullah K.J. , Khafaji Hajar A. H.
Published: November 2021

A field experiment was carried out at the second agricultural research and experiment station of the College of Agriculture, Muthanna University, for the 2019-2020 agricultural season, with the randomized complete block design RCBD, using two factors and three repeats, that’s to study the effect of adding the bio inoculant from Bacillus megaterium bacteria, and when loaded the bacterium with the immobilization inoculation technology on zeolite, sodium alginate, Agarose and bentonite and it’s symboled of M0, M1, M2 and M3 respectively to compare its efficiency in increasing potassium available and growth of wheat plant variety Eba’a 99. The experiment included two comparison treatments, the first being B0 without the addition of the bacterial inoculant and the second comparative treatment being B1 adding the bacterial vaccine. At the end of the experiment, potassium concentration was estimated in soil after cultivation. The results showed a clear moral effect of the use of the immobilized bacterial inoculant in Nitrogen available at a 15.65 (mg N kg−1 soil) and with an increase of 17.14%, Potassium available at a 289.2 (mg K kg−1 soil) and an increase of 6.79%, and the plant height was a rate of 84.87 cm and an increase of 9.41% and bio yield at 810.25 kg dunum−1 and an increase of 34.98%.
The Effect of Some Chemical Compounds and Plants Water Extracts on Inhibiting The Nitrification in The Soil and Wheat (Triticum Aestivuim L.) Growth and Yield
Authors: Al-Barakat Hanoon N.Kadhem , Neghamish Razzaq ghazi , Al-Shujairy Qassim A.T.
Published: November 2021

A field experiment was carried out in Dhi Qar Governorate, Al-Fadhliya region, for season of 2018-2019. Chemical compounds DMPP, DCD, and ATS as well as aqueous extracts of capers seeds and palm bast, were added to inhibiting the nitrification in the soil, and some of the growth characteristics of the wheat. Three of nitrogen level were added as urea (46% N) fertilizer (100, 150 and 200 kg N per ha). Aqueous extracts of plants were added to the urea fertilizer at a concentration of 100 ml for each kg of fertilizer. The experiment designed used RCBD with three replications. Wheat seeds were sown at 11/15/2018. Soil samples were Collecting from the soil (0-30) cm during the growing season after (10, 20, 40 and 60) days after the fertilization. The amount of ammonium, nitrate and nitrite, were estimated. The results showed that the fertilizer level 150 kg N ha−1 with all extracts and chemical compound treatments were exceeded compared with 200 kg N ha−1 without treatments.
The Effect of Humic Acid, Vermicompost and Nano-Phosphorous on Growth and Yield Characteristics of Maize (Zea mays L.)
Authors: Al-Taweel Luma Salih Jabbar , Al-Saadawi Ahmed Malik Waheed
Published: November 2021

In order to study the effect of adding humic acid, vermicompost and nano-phosphorous on the growth characteristics and yield of maize. An experiment was carried out in one of the fields located in Afak sub-district - Diwaniyah Governorate - Iraq in the autumn season 2020.

The experiment was carried out according to a Complete Randomized Blocks Design with three replications. The treatments included adding humic acid at three levels (0, 10 and 20) kg H−1 and coded (H0, H1 and H2) sequentially, while vermicompost was added at two levels (0 and 4) tons H−1 and coded (V0 and V1) sequentially. While nano-phosphorous was added at three levels (0, 5 and 10) kg H−1 that coded by (nP0, nP1 and nP2) sequentially.

The results of the experiment showed outperform the fertilizer combination (VnP1), which consisted of vermicompost (4) H−
1ton and nano-phosphorous (5) kgH−1, as it recorded the highest content of chlorophyll in leaves, the highest plant height, the highest weight of the vegetative and root system, the percentage of protein and the total grain yield (66.53). SPAD and 269.93 cm, 53.53 g and 11.853 g) compared to the control treatment that recorded the lowest values, followed by treatment (V) with a single effect of vermicompost (4) tonH−1, which outperformed in the content of leaves from chlorophyll, plant height, dry weight of the vegetative and root system and the percentage of the protein and total yield which recorded (SPAD 65.77, 263.50 cm, 53.04 g, 11.520 g, 12.25% and 12,393 mcg H−1) compared to the control treatment that recorded the lowest values, as the second level of single nano-phosphorous fertilizer (nP2) was significantly superior compared to the levels addition of nP and comparison treatment.
Study of The Effect of Salt Stress and Kinetin and Their Interaction on The Growth and Yield of Wheat (Triticum Aestivum L.)
Authors: Al-Khafaji Zahra Hussein , Al-Burki Fouad Razzaq
Published: November 2021

A field experiment was conducted at the first station of the College of Agriculture/University of Al-Muthanna for the agricultural season 2020-2021, with the aim of studying the effect of treatment with salinity stress and kinetin on the growth and yield of the wheat (Triticum aestivum L.) cultivar of Bohooth 22. The experiment was applied by split plates design using a randomized complete block design (R.C.B.D) with three Replicators of 36 experimental units The main units included levels of irrigation water salinity (2.5, 5, 7.5, 10) ds/m, while the secondary units included levels of kinetin (0, 30, 60 Ppm). The results of the statistical analysis showed a significant difference in the salinity of the high irrigation water in most growth traits such as plant height, flag leaf area, number of tillers plant−1, spike length (cm) and number of days to physiological maturity (day) at a rate of (.5473, 14.912, 3.222, 9.176, 143.67) respectively, and the traits of the yield and its components represented by the number of spikes. m2, number of grains per spike, weight of 1000 grains (gm), grain yield (ton ha−1) and biological yield (ton ha−1) at a rate of (300.06, 35.39, 31.60, 3.52, 9.46) respectively, while soaking the seeds with kinetin led to a significant increase in most of the studied traits. Thus, we conclude that salt stress has a negative role on the growth stages of the vegetative plant, and this leads to the reduction of the yield and its components.
Effect of Phosphate Fertilization and Iron Spraying on Growth Parameter and Yield of Oat (Avena Sativa L.)
Authors: Alabdalsayid Kadhm K.A. , Al-Freeh Lamiaa M.S.
Published: November 2021

A field experiment was conducted during the agricultural season 2020-2021 at the Agricultural Research Station/College of Agriculture/University of Basra (Al-Haritha site) (20 km from the center of Basra Governorate). To study the effect of four levels of phosphate fertilizer (P0=0, P1=50, P2=100 and P3=150 Kg ha-1) and four concentrations of iron spray(F0=0, F1=1000, F2=2000 and F3=3000 PPM). on the growth, yield and quality of oats (Avena sativa L.) Janzania cultivar the experiment was carried out in a split-plot arrangementusinga randomized complete block design (RCBD) with three replications. Phosphate fertilizer levels occupied the main plot, and iron concentrations occupied the sub-plots. The results showed that the P3 level was significantly superior in all the studied traits, which gave the highest grain yield of 6.13 mcg ha-0. The concentration F2 was significantly superior in all the studied traits, which gave the highest grain yield of 5.29 mcg ha-0. The interaction also showed the superiority of the combination P3*F2 in plant height, flag leaf area, number of branches and grain yield, while the interaction was not significant in the trait of leaf area index and Net Assimilation rate and crop growth rate
Modelling adhesively-bonded T-joints by a meshless method
Authors: Sánchez I J , Ramalho L D C , Campilho R D S G , Belinha J
Published: November 2021

Bonding of non-parallel substrates has many applications in the transport industry. Adhesively-bonded T-joints are employed for that purpose. However, geometrical dimensions, substrates’ shape and material choices are broad. The effect that varying upper substrate thickness has on the joint strength (P

max
) was investigated in this work through numerical analyses. The numerical analysis was performed using a meshless method, the natural neighbour radial point interpolation method (NNRPIM), which has been proven accurate and robust in another adhesive joint configuration. Materials were considered elastic-plastic. A yield criterion developed for rubber-like materials, the Exponent Drucker-Prager, was used for the adhesive layer, while the metallic substrates were analysed with the von Mises yield criterion. P

max
was determined numerically using a strain-based continuum mechanics failure criterion. Normalised peel and shear stress distributions along the bond-line are presented. Effective strains, both elastic and plastic, were also obtained. The estimated P

max
was compared with experimental data; a good agreement was found. The stress distribution along the bond line becomes asymmetric in joints with unbalanced substrate thicknesses. At P

max
, from 10 to 25% of the bond-line has entered into plastic regime. The results indicate that the proposed methodology is suitable to analyse adhesively-bonded joints under different load solicitations.
From single layer to multilayer networks in mild cognitive impairment and Alzheimer’s disease
Authors: Echegoyen Ignacio , López-Sanz David , Maestú Fernando , Buldú Javier M
Published: November 2021

We investigate the alterations of functional networks of patients suffering from mild cognitive impairment and Alzheimer’s disease (AD) when compared to healthy individuals. Departing from the magnetoencephalographic recordings of these three groups, we construct and analyse the corresponding single layer functional networks at different frequency bands, both at the sensors and the regions of interest (ROI) levels. Different network parameters show statistically significant differences, with global efficiency being the one having the most pronounced differences between groups. Next, we extend the analyses to the frequency-band multilayer networks (MN) of the same dataset. Using the mutual information as a metric to evaluate the coordination between brain regions, we construct the αβ MN and analyse their algebraic connectivity at baseline λ
2−BSL
(i.e., the second smallest eigenvalue of the corresponding Laplacian matrices). We report statistically significant differences at the sensor level, despite the fact that these differences are not clearly observed when networks are obtained at the ROIs level (i.e., after a source reconstruction procedure). Next, we modify the weights of the inter-links of the multilayer network to identify the value of the algebraic connectivity λ
2−T
leading to a transition where layers can be considered to be fully merged. However, differences between the values of λ
2−T
of the three groups are not statistically significant. Finally, we developed nested multinomial logistic regression models (MNR models), with the aim of predicting group labels with the parameters extracted from the MN (λ
2−BSL
and λ
2−T
). Using these models, we are able to quantify how age influences the risk of suffering AD and how the algebraic connectivity of frequency-based multilayer functional networks could be used as a biomarker of AD in clinical contexts.
TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine
Authors: Li Peng , Zhang Haoran , Zhang Wuxia , Zhang Yuanyuan , Zhan Lingmin , Wang Ning , Chen Caiping , Fu Bangze , Zhao Jinzhong , Zhou Xuezhong , Guo Shuzhen , Chen Jianxin
Published: November 2021

One of the most difficult problems that hinder the development and application of herbal medicine is how to illuminate the global effects of herbs on the human body. Currently, the chemo-centric network pharmacology methodology regards herbs as a mixture of chemical ingredients and constructs the ‘herb-compound-target-disease’ connections based on bioinformatics methods, to explore the pharmacological effects of herbal medicine. However, this approach is severely affected by the complexity of the herbal composition. Alternatively, gene-expression profiles induced by herbal treatment reflect the overall biological effects of herbs and are suitable for studying the global effects of herbal medicine. Here, we develop an online transcriptome-based multi-scale network pharmacology platform (TMNP) for exploring the global effects of herbal medicine. Firstly, we build specific functional gene signatures for different biological scales from molecular to higher tissue levels. Then, specific algorithms are designed to measure the correlations of transcriptional profiles and types of gene signatures. Finally, TMNP uses pharmacotranscriptomics of herbal medicine as input and builds associations between herbs and different biological scales to explore the multi-scale effects of herb medicine. We applied TMNP to a single herb Astragalus membranaceus and Xuesaitong injection to demonstrate the power to reveal the multi-scale effects of herbal medicine. TMNP integrating herbal medicine and multiple biological scales into the same framework, will greatly extend the conventional network pharmacology model centering on the chemical components, and provide a window for systematically observing the complex interactions between herbal medicine and the human body. TMNP is available at http://www.bcxnfz.top/TMNP.
The Crown’s Ecclesiastical Creditors: Loans from the English Church to Edward II and Edward III, 1307–1377
Authors: McCallum Robin
Published: November 2021

This article examines the loans made by the English Church to the Crown between 1307 and 1377 to finance the defence of the kingdom. It traces the origins of this policy to the political crisis of 1310–11, highlighting how Edward II approached his subjects for loans in order to circumvent the Ordainers’ restrictions on purveyance. Setting them in the context of the wars with France and Scotland, it considers when and why loans became a common demand on the Church. Clergymen, however, were not substantial royal creditors and lent, at most, £50,000–£60,000 in money and victuals during this period. This article assesses why ecclesiastics agreed or refused to provide loans, and why Edward II and Edward III failed to develop them into important creditors. Essentially, the Crown encountered three groups of ecclesiastical creditors: a few prelates and abbots with close political ties to the king who lent extraordinary sums; a small group who pleaded poverty or lent negligible amounts; and numerous clergymen who were far from enthusiastic, but who lent an acceptable amount either for rewards or to keep the peace with the king. The Crown’s struggles in securing loans of considerable value were partly the result of its excessive taxation demands on the Church. But many clergymen also viewed loans as another attempt by a secular power to interfere with ecclesiastical privileges. Their reluctance to provide loans stemmed from their claims of liberty from secular interference, part of a wider, long-standing and pan-European struggle between the Church and secular powers.
Development of affinity bead–based in vitro metal–ligand binding assay reveals dominant cadmium affinity of thiol-rich small peptides phytochelatins beyond glutathione
Authors: Uraguchi Shimpei , Nagai Kenichiro , Naruse Fumii , Otsuka Yuto , Ohshiro Yuka , Nakamura Ryosuke , Takanezawa Yasukazu , Kiyono Masako
Published: November 2021

For a better understanding of metal–ligand interaction and its function in cells, we developed an easy, sensitive, and high-throughput method to quantify ligand–metal(loid) binding affinity under physiological conditions by combining ligand-attached affinity beads and inductively coupled plasma-optical emission spectrometry (ICP-OES). Glutathione (GSH) and two phytochelatins (PC2 and PC3, small peptides with different numbers of free thiols) were employed as model ligands and attached to hydrophilic beads. The principle of the assay resembles that of affinity purification of proteins in biochemistry: metals binding to the ligand on the beads and the rest in the buffer are separated by a spin column and quantified by ICP-OES. The binding assay using the GSH-attached beads and various metal(loid)s suggested the different affinity of the metal–GSH interactions, in accordance with the order of the Irving–Williams series and the reported stability constants. The binding assay using PC2 or PC3-attached beads suggested positive binding between PCs and Ni(II), Cu(II), Zn(II), Cd(II), and As(III) in accordance with the number of thiols in PC2 and PC3. We then conducted the competition assay using Cd(II), Mn(II), Fe(II), Cu(II), and Zn(II), and the results suggested a better binding affinity of PC2 with Cd(II) than with the essential metals. Another competition assay using PC2 and GSH suggested a robust binding affinity between PCs and Cd(II) compared to GSH and Cd(II). These results suggested the dominance of PC-Cd complex formation in vitro, supporting the physiological importance of PCs for the detoxification of cadmium in vivo. We also discuss the potential application of the assay.
Identifying Crystal Accumulation in Granitoids through Amphibole Composition and In Situ Zircon O Isotopes in North Qilian Orogen
Authors: Chen Shuo , Niu Yaoling , Wang Xiaohong , Xue Qiqi , Sun Wenli
Published: November 2021

Granitoids are the main constituents of the continental crust, and an understanding of their petrogenesis is key to the origin and evolution of continents. Whether crystal fractionation is the dominant way to generate evolved magmas has long been debated, mostly because such processes would produce large volumes of complementary cumulates, which remains elusive. Mafic magmatic enclaves (MMEs) are ubiquitous in granitoids and their presence was initially recognized as cumulates. However, because many MMEs lack obvious evidence of accumulation, such as the classic cumulate textures and modal layering, the cumulate origin of MMEs has been abandoned and the model of magma mixing between mafic and felsic magmas has become popular. In this study, we conduct a combined study of amphibole composition and in situ O isotopes in zircons on three suites of orogenic granitoids with MMEs from the North Qilian Orogenic Belt (NQOB). We find that the MMEs and their host granodiorites show overlapping zircon δ18O values, affirming that they share the same parental magmas. The amphibole compositions indicate that amphiboles from the MMEs are not in equilibrium with a melt whose composition was that of the bulk-rock. These new data, together with the published bulk-rock data, suggest that the MMEs in our study have clear cumulate signatures and are thus of cumulate origin. Our study provides evidence for crystal accumulation in granitoids in the NQOB. This new understanding calls for re-examination on the petrogenesis of some intermediate magmatic rocks (granitoid/andesite) in discussing models of continental crustal growth.
Biochemical characteristics and demography of the marine calanoid copepod Calanus finmarchicus during spring in Icelandic waters
Authors: Th Eysteinsson Stefán , Jónasdóttir Sigrún H , Gislason Astthor , Gudmundsson Kristinn , Olafsdottir Solveig R , Arason Sigurjón , Gudjónsdóttir María
Published: November 2021

The chemical composition of Calanus finmarchicus was analyzed at 21 stations from three regions where 12 transects were sampled from 0 to 50 m depth, including stage composition analysis at the Siglunes and Selvogsbanki transects in relation to the effects of different water masses, during a survey in Icelandic waters during 11–29 May 2018. The stage composition of C. finmarchicus at the northern transect of Siglunes was mostly made up of copepodites CI–CIII, around 76%, whereas older copepods CV–CVI dominated, around 64%, at the southern transect of Selvogsbanki. The dry weight (dw) and lipid content of C. finmarchicus were overall highest in the southwest (160 ± 60 μg dw ind−1 and 60 ± 20 μg lipids ind−1) and lowest in the east (120 ± 20 μg dw ind−1 and 30 ± 10 μg lipids ind−1). Total astaxanthin content ranged from 0.14 to 0.27 μg mg−1 dw. Chitin made up 2–4% of the dw. The diatom marker C20:5n3 was prolific in the copepods southwest of Iceland, while the dinoflagellate markers C18:4n3 and C22:6n3 dominated in the copepods east of Iceland. The results indicate that C. finmarchicus found in the south of Iceland developed faster than those in the north, with the variation in chemical composition and developmental time highly influenced by hydrographic regions.
Olanzapine intramuscular shows better efficacy than zuclopenthixol acetate intramuscular in reducing the need for restraint, but not in comparison to haloperidol intramuscular
Authors: Sinai Omri , Stryjer Rafael , Bloemhof-Bris Esther , Weizman Shira , Shelef Assaf
Published: November 2021

Many psychotic patients are treated with antipsychotic medications during acute agitation and aggressive behavior episodes in an attempt to achieve a rapid calming effect. Those medications include olanzapine, zuclopenthixol acetate, and haloperidol intramuscular administration. This study compared the effectiveness of these injections in reducing the need for restraint during agitated-psychotic episodes that include aggression. Sociodemographical and clinical data were retrieved from the electronic medical records of 179 patients who needed rapid calming while hospitalized in a mental health center with acute psychosis. The treatments administered were olanzapine intramuscular, zuclopenthixol acetate intramuscular, and haloperidol intramuscular. The assessed outcomes were rate of restraint and violent behavior. Olanzapine was found significantly more effective in reducing the need for restraint compared to zuclopenthixol acetate. No significant differences were found between haloperidol and the other two with regard to restraint. Neither were other significant differences found between the groups with regard to violent or self-harming behaviors. No significant differences were found in the rate of violent behavior and antipsychotic dosage at discharge. In conclusion, in inpatients with acute agitated psychosis, olanzapine intramuscular shows better efficacy in reducing the need for restraint, at least as compared to zuclopenthixol acetate intramuscular.
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis
Authors: Peker Nilay , Schuele Leonard , Kok Nienke , Terrazos Miguel , Neuenschwander Stefan M. , de Beer Jessica , Akkerman Onno , Peter Silke , Ramette Alban , Merker Matthias , Niemann Stefan , Couto Natacha , Sinha Bhanu , Rossen John WA
Published: November 2021

Whole-genome sequencing (WGS) of

Mycobacterium tuberculosis

(MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis (TB) and for outbreak investigations. We evaluated the performance of long-read (LR) and/or short-read (SR) sequencing for anti-TB drug-resistance prediction using the TBProfiler and Mykrobe tools, the fraction of genome recovery, assembly accuracies and the robustness of two typing approaches based on core-genome SNP (cgSNP) typing and core-genome multi-locus sequence typing (cgMLST). Most of the discrepancies between phenotypic drug-susceptibility testing (DST) and drug-resistance prediction were observed for the first-line drugs rifampicin, isoniazid, pyrazinamide and ethambutol, mainly with LR sequence data. Resistance prediction to second-line drugs made by both TBProfiler and Mykrobe tools with SR- and LR-sequence data were in complete agreement with phenotypic DST except for one isolate. The SR assemblies were more accurate than the LR assemblies, having significantly (P<0.05) fewer indels and mismatches per 100 kbp. However, the hybrid and LR assemblies had slightly higher genome fractions. For LR assemblies, Canu followed by Racon, and Medaka polishing was the most accurate approach. The cgSNP approach, based on either reads or assemblies, was more robust than the cgMLST approach, especially for LR sequence data. In conclusion, anti-TB drug-resistance prediction, particularly with only LR sequence data, remains challenging, especially for first-line drugs. In addition, SR assemblies appear more accurate than LR ones, and reproducible phylogeny can be achieved using cgSNP approaches.
Modeling the age distribution of retinoblastomas
Authors: Tetearing Alexandr N.
Published: November 2021

In this work, based on real data on the size of the eyeball (in a fetus, in a child, and in young people under 20), we constructed a model function of the growth of the retinal cell tissue.

We used this function to construct a theoretical age distribution of retinoblastomas. We constructed theoretical age distributions for four different models of retinoblastoma: a complex mutational model, a third mutational model, a model with a sequence of key events, and a model of a single oncogenic event with two different latencies (hereditary and non-hereditary retinoblastoma).

We compared the theoretical age distribution of retinoblastomas with the real age distribution based on SEER data (Surveillance Epidemiology and End Results; program of the American National Cancer Institute). In total, we examined 843 cases in women and 908 cases in men.

For all models (separately for women and men), we obtained estimates of the following cancer parameters: the specific frequency of key events (events that trigger cancer); the duration of the latency period of cancer; the number of key events required for cancer to occur.

For the composite age distributions, we calculated the theoretical mean age at diagnosis for hereditary and non-hereditary retinoblastomas.

The best approximation accuracy (for male and female forms of retinoblastoma) is shown by a model with a sequence of key events.
Collective polymerase dynamics emerge from DNA supercoiling during transcription
Authors: Sevier Stuart A. , Hormoz Sahand
Published: November 2021

All biological processes ultimately come from physical interactions. The mechanical properties of DNA play a critical role in transcription. RNA polymerase can over or under twist DNA (referred to as DNA supercoiling) when it moves along a gene resulting in mechanical stresses in DNA that impact its own motion and that of other polymerases. For example, when enough supercoiling accumulates, an isolated polymerase halts and transcription stops. DNA supercoiling can also mediate non-local interactions between polymerases that shape gene expression fluctuations. Here, we construct a comprehensive model of transcription that captures how RNA polymerase motion changes the degree of DNA supercoiling which in turn feeds back into the rate at which polymerases are recruited and move along the DNA. Surprisingly, our model predicts that a group of three or more polymerases move together at a constant velocity and sustain their motion (forming what we call a polymeton) whereas one or two polymerases would have halted. We further show that accounting for the impact of DNA supercoiling on both RNA polymerase recruitment and velocity recapitulates empirical observations of gene expression fluctuations. Finally, we propose a mechanical toggle switch whereby interactions between genes are mediated by DNA twisting as opposed to proteins. Understanding the mechanical regulation of gene expression provides new insights into how endogenous genes can interact and informs the design of new forms of engineered interactions.

PACS numbers:
Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
Authors: Ugolini Camilla , Mulroney Logan , Leger Adrien , Castelli Matteo , Criscuolo Elena , Williamson Maia Kavanagh , Davidson Andrew D , Almuqrin Abdulaziz , Giambruno Roberto , Jain Miten , Frige Gianmaria , Olsen Hugh , Tzertzinis George , Schildkraut Ira , Wulf Madalee G. , Corrêa Ivan R. , Ettwiller Laurence , Clementi Nicola , Clementi Massimo , Mancini Nicasio , Birney Ewan , Akeson Mark , Nicassio Francesco , Matthews David A. , Leonardi Tommaso
Published: November 2021

The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested sub genomic RNAs used to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5′ cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
CHIQUITA1 maintains temporal transition between proliferation and differentiation in Arabidopsis thaliana
Authors: Bossi Flavia , Jin Benjamin , Lazarus Elena , Cartwright Heather , Dorone Yanniv , Rhee Seung Y.
Published: November 2021

Body size varies widely among species, populations, and individuals depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared to wild type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a certain number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and physically and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination.

Significance

Timing of the transition between proliferation and differentiation is fundamental for determining the final size of organs and organisms. In agriculture, controlling organ and organism size can influence key agronomic traits such as yield and biomass. Dwarfism prevents lodging and was the trait responsible for the Green Revolution. Today, more sophisticated traits are needed for generating crops that are both resilient and sustainable. Revealing the molecular mechanisms that control the temporal transition between proliferation and differentiation will help unlock the potential of next-generation crops. Here, we report that CHIQUITA 1 in Arabidopsis thaliana is needed to maintain the proper timing of the transition between proliferation and differentiation in leaves and roots.
Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition
Authors: Reis Andre Martins , Hammond Jillian , Stevanovski Igor , Arnold Jonathon C , McGregor Iain S. , Deveson Ira , Gururajan Anand
Published: November 2021

Our understanding of the molecular pathology of posttraumatic stress disorder (PTSD) is rapidly evolving and is being driven by advances in sequencing techniques. Conventional short-read RNA sequencing (RNA-seq) is a central tool in transcriptomics research that enables unbiased gene expression profiling. With the recent emergence of Oxford Nanopore direct RNA-seq (dRNA-seq), it is now also possible to interrogate diverse RNA modifications, collectively known as the ‘epitranscriptome’. Here, we present our analyses of the male and female mouse amygdala transcriptome and epitranscriptome, obtained using parallel Illumina RNA-seq and Oxford Nanopore dRNA-seq, associated with the acquisition of PTSD-like fear induced by Pavlovian cued-fear conditioning. We report significant sex-specific differences in the amygdala transcriptional response during fear acquisition, and a range of shared and dimorphic epitranscriptomic signatures. Differential RNA modifications are enriched among mRNA transcripts associated with neurotransmitter regulation and mitochondrial function, many of which have been previously implicated in PTSD. Very few differentially modified transcripts are also differentially expressed, suggesting an influential, expression-independent role for epitranscriptional regulation in PTSD-like fear-acquisition. Overall, our application of conventional and newly developed methods provides a platform for future work that will lead to new insights into and therapeutics for PTSD.
Stable and functionally diverse versatile peroxidases by computational design directly from sequence
Authors: Barber-Zucker Shiran , Mindel Vladimir , Garcia-Ruiz Eva , Weinstein Jonathan J. , Alcalde Miguel , Fleishman Sarel J.
Published: November 2021

White-rot fungi secrete a repertoire of high-redox potential oxidoreductases to efficiently decompose lignin. Of these enzymes, versatile peroxidases (VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes for research and industrial use, but their recombinant production is extremely challenging. To date, only a single VP has been structurally characterized and optimized for recombinant functional expression, stability and activity. Computational enzyme optimization methods can be applied to many enzymes in parallel, but they require accurate structures. Here, we demonstrate that model structures computed by deep-learning based ab initio structure prediction methods are reliable starting points for one-shot PROSS stability-design calculations. Four designed VPs encoding as many as 43 mutations relative to the wild type enzymes are functionally expressed in yeast whereas their wild type parents are not. Three of these designs exhibit substantial and useful diversity in reactivity profile and tolerance to environmental conditions. The reliability of the new generation of structure predictors and design methods increases the scale and scope of computational enzyme optimization, enabling efficient discovery and exploitation of the functional diversity in natural enzyme families.
Lysophosphatidylcholine acyltransferase 2 (LPCAT2) Regulates The Expression of Macrophage Phenotype Markers in RAW264.7 Cells
Authors: Poloamina Victory Ibigo , Alrammah Hanaa , Abate Wondwossen , Avent Neil , Fejer Gyorgy , Jackson Simon K.
Published: November 2021

1

Macrophages are key antigen presenting cells that also secrete cytokines during inflammation. They can be polarised to M1 or M2 phenotypes. Molecules such as CD206 and inducible Nitric Oxide Synthase are considered macrophage phenotype markers because they are highly expressed in either M1 or M2 macrophages. LPCAT2 is a phospholipid modifying enzyme that influences inflammatory responses in macrophages. However, how LPCAT2 influences inflammation is not fully understood.

In this study, we have used genetic technology to study the influence of LPCAT2 on macrophage phenotype markers.

Our results show for the first time that overexpression of LPCAT2 promotes the expression of M1 macrophage phenotype markers, and attenuates the expression of M2 macrophage markers.
Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination
Authors: Arvindekar Shreyas , Jackman Matthew J. , Low Jason K.K. , Landsberg Michael J. , Mackay Joel P. , Viswanath Shruthi
Published: November 2021

The Nucleosome Remodeling and Deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC-MALLS, DIA-MS, XLMS, negative-stain EM, X-ray crystallography, NMR spectroscopy, secondary structure predictions and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4 (MHR), MTA1N-HDAC1-MBD3GATAD2CC (MHM), and MTA1-HDAC1-RBBP4-MBD3-GATAD2A (NuDe). The integrative structures were corroborated by examining independent crosslinks, cryo-EM maps, biochemical assays, known cancer-associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack-knifing. Localization of the full-length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1C-MTA1BAH, MTA1BAH-MBD3MBD, and HDAC160-100-MBD3MBD. Our approach also allowed us to localize regions of unknown structure, such as HDAC1C and MBD3IDR, thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far.
Supplementary motor area contributions to rhythm perception
Authors: Leow Li-Ann , Rinchon Cricia , Emerick Marina , Grahn Jessica A.
Published: November 2021

Timing is everything, but our understanding of the neural mechanisms of timing remains limited, particularly for timing of sequences. Temporal sequences can be represented relative to a recurrent beat (beat-based or relative timing), or as a series of absolute durations (non-beat-based or absolute timing). Neuroimaging work suggests involvement of the basal ganglia, supplementary motor area (SMA), the premotor cortices, and the cerebellum in both beat- and non-beat-based timing. Here we examined how beat-based timing and non-beat-based sequence timing were affected by modulating excitability of the supplementary motor area, the right cerebellum, and the bilateral dorsal premotor cortices, using transcranial direct current stimulation (tDCS). Participants were subjected to a sham stimulation session, followed an active stimulation session where anodal or cathodal 2mA tDCS was applied to the SMA, right premotor cortex, left premotor cortex, or the cerebellum. During both sessions, participants discriminated changes in rhythms which differentially engage beat-based or non-beat-based timing. Rhythm discrimination performance was improved by increasing SMA excitability, and impaired by decreasing SMA excitability. This polarity-dependent effect on rhythm discrimination was absent for cerebellar or premotor cortex stimulation, suggesting a crucial role of the SMA and/or its functionally connected networks in rhythmic timing mechanisms.