bluuebunny/crossref_metadata_2025 huggingface dataset:
Peculiarities of breeding work with red foxes obtained as a result of dominant color mutations
Authors: Balakirev N A , Shumilina N N , Larina E E , Galatskaya A A
Published: September 2021

The proportion of the silver-black breed population in the fox gene pool by 2019 was 89.3%, the Vyatka ognevka accounted for 9.9%, so only 0.8% remained for the entire colored population. However, it is no secret that the market does not tolerate uniformity. One of the most effective ways to increase sales of any product, including fur products, is to expand the assortment. The fox industry has something to offer the consumer: in the niche of fur farming by the variety of colorful forms with it can be compared only with mink. Unfortunately, despite the fact that the history of "color" fox breeding dates back to the 30s of the last century, at present there is a lack of systematized information in Russian on various aspects of breeding mutant color forms of the fox. This work is devoted to determining the optimal breeding methods for obtaining the maximum number of young foxes of original coloration obtained as a result of dominant mutations. Research objective is to reveal and generalize the peculiarities of breeding work with foxes of snow, white-marbled, platinum and marbled colors. To this end, the following tasks have been set: to analyze the reproduction rates of female and male foxes of the above colors; to compare the results of reproduction depending on age; to identify the most productive type of crossbreeding for the breeding of the foxes presented. The article presents the results of various interbreeding of silver-black, snow, marbled and red foxes. Analysis of mating of animals of different ages has been carried out. The optimal combinations of parental pairs are revealed.
Polymorphism of genes among heifers with different types of constitution
Authors: Tyulebaev S D , Kadysheva M D
Published: September 2021

The article presents the results of the manifestation of the polymorphic state of single nucleotide (SNP) genes CAPN1 and TG5 among 15-16 month old heifers of the Bredy meat type simmentals, evenly distributed over the constitution of the body type. For the study, the real-time PCR method was used with the using of oligonucleotide primers (GenBank) on an Applied Biosistems 3130 automatic DNA sequencer using a standard protocol with forward and reverse primers. In animals, in the corresponding constitutional ranks, the growth rates and the state of meat forms at the age of 15 months were studied in a comparative aspect. Significant differences were revealed in the assessment of meat forms of leptosomal and eirosomal animals in favor of more significant points in eirosomal animals. For the dense type, this superiority was 4.4 points (P <0.01), and for the loose type, respectively, 5.2 points (P <0.01). The results of genotyping revealed some interesting facts. If the even distribution of genotypes according to constitutional types was determined by the CAPN1 gene, then the TG5 gene was characterized by their significant displacement. Thus, the homozygous desired TT genotype of this gene, determined in 7.5% of the animals in the sample, was found only in heifers with a loose constitution type, and 2/3 of them were found in the group of eirosome animals. Consequently, for eirosome animals with a loose type of constitution, predominant saturation of DNA with the T allele of the TG5 gene is characteristic, which may be a sign of a possible manifestation of beef marbling associated with this gene.
Impact of the seeding rate on the yield and its quality of the new sunflower hybrids
Authors: Bushnev A S , Borisenko O M , Mamyrko Yu V , Gridnev A K
Published: September 2021

The effect of different seeding rates, providing the density of 40, 60, and 80 thousand plants/ha, on the yield and its quality of the new sunflower hybrids of VNIIMK breeding (Immi, Arneb, Gorfild) was studied at the V.S. Pustovoit All-Russian Research Institute of Oil Crops (VNIIMK) (Krasnodar) in 2019-2020. The purpose of the research is to determine the effect of different seeding rates on the elements of plant productivity, yield, oil content of seeds, and oil yield of promising sunflower hybrids. The sunflower hybrid Arneb appeared to be the most stable in terms of productivity at different seeding rates. It has a high tolerance to its increase even under a water deficiency. Hybrids Immi and Gorfild are more susceptible to plant thickening. Their productivity is decreasing in unfavorable water conditions.
Dynamics of productive qualities of rabbits when creating a new breeding group
Authors: Kosovsky G Yu , Karelina T K , Shumilina A R , Golovanova E V
Published: September 2021

Many branches of animal husbandry in our country are in need of domestic highly productive breeds and types of animals. Along with other problems – the lack of domestic developments in the field of animal housing and feeding systems that ensure high production efficiency, the lack of high-quality breeding resources is the most important factor hindering the development of the population’s own food production. Technologies and breeding resources of animals borrowed from other countries lead to short-term effects of the development of livestock industries. Rabbit breeding is no exception – the branch of animal husbandry that allows you to get dietary meat at a fast pace. Since the 1940s of the XX century, NIIPZK has been providing scientific support for the formation and development of the rabbit breeding industry. In particular, the scientists of the institute carried out work on breeding. With the participation of the Institute’s employees, the Soviet Chinchilla rabbit breed was created and the White Giant breed was significantly improved. To increase the efficiency of rabbit breeding, different two- and three-breed crosses were tested. Since the 1970s of the last century, no work has been carried out to create new crosses of meat-skin and meat breeds of rabbits. The last rabbit breed approved by the Ministry of Agriculture of Russia (2014) was a decorative breed-the Russian dwarf Angora. Currently, rabbit breeding uses breeding resources imported from abroad, which makes the farms dependent and leads to serious financial costs. Therefore, the actual directions in the selection of domestic rabbit breeding are the creation of new domestic highly productive breeds, types, and crosses. The article presents the results of the creation of a breeding group of rabbits to obtain a new breed. The breeding group was created using at the first stage animals of the parental form of the three-breed cross of Spring rabbits, conducting further breeding "in itself" and selecting from the offspring from the best pairs of individuals that meet the target criteria.
Effect of genotype on the development pattern of muscles and muscle groups in steers at the age of 18 months
Authors: Zhaimysheva S S , Kosilov V I , Voroshilova L N , Gerasimova T G , Klyukvina Ye Yu
Published: September 2021

The development patterns of carcass muscles were studied on Simmental and Black-Spotted steers and their hybrids of the 1st generation. At the age of 18 months, a control slaughter of 3 steers of different genotypes was carried out: Group I - purebred Simmental steers; Group II - hybrids of ½ Simmentals x ½ Red Steppe steers; Group III - hybrids of ½ Simmentals x ½ Black-Spotted steers. To study the muscle groups and individual muscles development according to anatomical regions, the left half-carcasses were prepared, taking into account the methodological instructions, and to facilitate the analysis of the material, the muscles were grouped according to the joints associated with them and the topographic location, using the generally accepted scheme. The muscles development was studied on the basis of the absolute mass indices of individual muscles and muscle groups. It was established that steers of Group III had the following advantages over the animals of the same age in Groups I and II: in the total muscle mass of the spinal column the advantage was 217-772 g (1.43 - 18.30%), in the total muscle mass of the shoulder girdle - 1.45-0.51 kg (9.78-3.51 %), the thoracic limb - 231-660g (14.37-41.04%), the pelvic limb - 3.16-1.11 kg (9.78-3.45%) and in general for the entire half-carcass of the recorded muscles - 6.62-2.33 kg (9.79-3.44 %).
Integrating terrestrial laser scanning with functional–structural plant models to investigate ecological and evolutionary processes of forest communities
Authors: O’Sullivan Hannah , Raumonen Pasi , Kaitaniemi Pekka , Perttunen Jari , Sievänen Risto
Published: September 2021

Background

Woody plants (trees and shrubs) play an important role in terrestrial ecosystems, but their size and longevity make them difficult subjects for traditional experiments. In the last 20 years functional–structural plant models (FSPMs) have evolved: they consider the interplay between plant modular structure, the immediate environment and internal functioning. However, computational constraints and data deficiency have long been limiting factors in a broader application of FSPMs, particularly at the scale of forest communities. Recently, terrestrial laser scanning (TLS), has emerged as an invaluable tool for capturing the 3-D structure of forest communities, thus opening up exciting opportunities to explore and predict forest dynamics with FSPMs.

Scope

The potential synergies between TLS-derived data and FSPMs have yet to be fully explored. Here, we summarize recent developments in FSPM and TLS research, with a specific focus on woody plants. We then evaluate the emerging opportunities for applying FSPMs in an ecological and evolutionary context, in light of TLS-derived data, with particular consideration of the challenges posed by scaling up from individual trees to whole forests. Finally, we propose guidelines for incorporating TLS data into the FSPM workflow to encourage overlap of practice amongst researchers.

Conclusions

We conclude that TLS is a feasible tool to help shift FSPMs from an individual-level modelling technique to a community-level one. The ability to scan multiple trees, of multiple species, in a short amount of time, is paramount to gathering the detailed structural information required for parameterizing FSPMs for forest communities. Conventional techniques, such as repeated manual forest surveys, have their limitations in explaining the driving mechanisms behind observed patterns in 3-D forest structure and dynamics. Therefore, other techniques are valuable to explore how forests might respond to environmental change. A robust synthesis between TLS and FSPMs provides the opportunity to virtually explore the spatial and temporal dynamics of forest communities.
Into Collabs: Public Applied Linguistics and Hip Hop Language Technicians
Authors: Williams Quentin
Published: September 2021

In this article, I propose the idea of public applied linguistics: that is, a type of applied linguistics that sees applied linguists doing the work of activism, with language activists, in the public, are (i) invested in the artistic representation of linkages between language reinvention and new relationalities, and (ii) highlighting, documenting and framing interventionist debates around language. Public applied linguists encounter, discourse with ‘language technicians’, expert-like language activists working with new visions of language on the periphery of post-apartheid South Africa, to think language otherwise and as a critical historical process, continually reinvented through the unique, creative, and dynamic practices of multilingualism to attain linguistic justice.
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data
Authors: Wong Christina , Li Bo
Published: September 2021

T cells participate directly in the body's immune response to cancer, allowing immunotherapy treatments to effectively recognize and target cancer cells. We previously developed DeepCAT to demonstrate that T cells serve as a biomarker of immune response in cancer patients and can be utilized as a diagnostic tool to differentiate healthy and cancer patient samples. However, DeepCAT’s reliance on tumor bulk RNA-seq samples as training data limited its further performance improvement. Here, we benchmarked a new approach, AutoCAT, to predict tumor-associated TCRs from targeted TCR-seq data as a new form of input for DeepCAT, and observed the same level of predictive accuracy.

Availability and implementation

Source code is freely available at https://github.com/cew88/AutoCAT, and data is available at 10.5281/zenodo.5176884.

Supplementary information

Supplementary data are available at Bioinformatics online.
Translating genetic and functional data into clinical practice: a series of 223 families with myotonia
Authors: Suetterlin Karen , Matthews Emma , Sud Richa , McCall Samuel , Fialho Doreen , Burge James , Jayaseelan Dipa , Haworth Andrea , Sweeney Mary G , Kullmann Dimitri M , Schorge Stephanie , Hanna Michael G , Männikkö Roope
Published: September 2021

High-throughput DNA sequencing is increasingly employed to diagnose single gene neurological and neuromuscular disorders. Large volumes of data present new challenges in data interpretation and its useful translation into clinical and genetic counselling for families. Even when a plausible gene is identified with confidence, interpretation of the clinical significance and inheritance pattern of variants can be challenging. We report our approach to evaluating variants in the skeletal muscle chloride channel ClC-1 identified in 223 probands with myotonia congenita as an example of these challenges. Sequencing of CLCN1, the gene that encodes CLC-1, is central to the diagnosis of myotonia congenita. However, interpreting the pathogenicity and inheritance pattern of novel variants is notoriously difficult as both dominant and recessive mutations are reported throughout the channel sequence, ClC-1 structure-function is poorly understood and significant intra- and interfamilial variability in phenotype is reported.

Heterologous expression systems to study functional consequences of CIC-1 variants are widely reported to aid the assessment of pathogenicity and inheritance pattern. However, heterogeneity of reported analyses does not allow for the systematic correlation of available functional and genetic data. We report the systematic evaluation of 95 CIC-1 variants in 223 probands, the largest reported patient cohort, in which we apply standardized functional analyses and correlate this with clinical assessment and inheritance pattern. Such correlation is important to determine whether functional data improves the accuracy of variant interpretation and likely mode of inheritance.

Our data provide an evidence-based approach that functional characterization of ClC-1 variants improves clinical interpretation of their pathogenicity and inheritance pattern, and serve as reference for 34 previously unreported and 28 previously uncharacterized CLCN1 variants. In addition, we identify novel pathogenic mechanisms and find that variants that alter voltage dependence of activation cluster in the first half of the transmembrane domains and variants that yield no currents cluster in the second half of the transmembrane domain. None of the variants in the intracellular domains were associated with dominant functional features or dominant inheritance pattern of myotonia congenita.

Our data help provide an initial estimate of the anticipated inheritance pattern based on the location of a novel variant and shows that systematic functional characterization can significantly refine the assessment of risk of an associated inheritance pattern and consequently the clinical and genetic counselling.
Are cognition and personality related in budgerigars?
Authors: Chen Jiani , Chen Lu , Yan Chuan , Yu Zibo , Zou Yuqi , Sun Yue-Hua
Published: September 2021

In recent years, researchers have been attempting to relate differences in personality (e.g., boldness, aggressiveness, exploration tendency) to variation in cognition (performances in tasks that require learning, reasoning, attention, or memory, etc.) both theoretically and empirically. However, it is unclear on what basis personality and cognition might be associated with each other. Previous theory suggests a connection between fast–slow personality types and cognitive speed–accuracy tradeoffs. In this study, we tested this hypothesis in budgerigars and found that, in their 1st associative learning, birds with fast personality (less fearful of handling stress) were fast learners in the beginning, while slow personality individuals improved faster, but both types of birds did not differ in accuracy. However, these relationships were context-dependent. No significant relationship was found in subsequent learning tasks (reversal learning and a 2nd associative learning) in the familiar context (task setup and apparatus similar to the 1st associative learning). We then conducted a problem-solving experiment with novel setup and apparatus to test 1 possible explanation that the association between personality and cognition in the 1st associative learning might be caused by noncognitive constraint, such as fearfulness when facing novel task setup and apparatus. We found that fast individuals interacted more with the problem box and solved it, whereas the slow birds were not. We suggest that personalities can influence cognitive performances and trigger a cognitive speed-improvement tradeoff under the novel context. However, there are no consistent cognitive styles that co-varied with different personalities.
Pyk2 suppresses contextual fear memory in an autophosphorylation-independent manner
Authors: Zheng Jin , Suo Lun , Zhou Yuxiao , Jia Liling , Li Jingwei , Kuang Yanping , Cui Donghong , Zhang Xuehong , Wu Qiang
Published: September 2021

Clustered protocadherins (Pcdhs) are a large family of cadherin-like cell adhesion proteins that are central for neurite self-avoidance and neuronal connectivity in the brain. Their downstream nonreceptor tyrosine kinase Pyk2 (proline-rich tyrosine kinase 2, also known as Ptk2b, Cakb, Raftk, Fak2, and Cadtk) is predominantly expressed in the hippocampus. We constructed Pyk2-null mouse lines and found that these mutant mice showed enhancement in contextual fear memory, without significant change in auditory-cued and spatial-referenced learning and memory. In addition, by preparing Y402F mutant mice, we observed that Pyk2 suppressed contextual fear memory in an autophosphorylation-independent manner. Moreover, using high-throughput RNA sequencing, we found that immediate early genes, such as Npas4, cFos, Zif268/Egr1, Arc, and Nr4a1, were enhanced in Pyk2-null mice. We further showed that Pyk2 disruption affected pyramidal neuronal complexity and spine dynamics. Thus, we demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2-null mice provide a model for understanding fear-related disorders. These findings have interesting implications regarding dysregulation of the Pcdh‒Pyk2 axis in neuropsychiatric disorders.
‘Capitalism: what has gone wrong?’: Who went wrong? Capitalism? The market economy? Governments? ‘Neoliberal’ economics?
Authors: Hellwig Martin
Published: September 2021

The paper contributes to a symposium of the Oxford Review of Economic Policy on ‘Capitalism: What has Gone Wrong, What Needs to Change, and How can it be Fixed?’. The analysis starts from the observation that, in the United States, the United Kingdom, and continental Europe, widespread discontent has become an important political force. I attribute this discontent to a sense of unfairness in developments of the past few decades. I relate this sense of unfairness to: (i) negative effects of structural change, including joblessness and regional decline, (ii) the observation of extraordinary growth in executive remuneration and financial-sector remuneration, coupled with government bailouts in the global financial crisis, and (iii) changes in public policy and public discourse, with a retrenchment of public services and public investment, except for bailouts and a focus on ‘efficiency’, the meaning of which is driven by the perceptions of corporate executives rather than standard welfare economics. To capture these developments, one needs to think about ‘capitalism’ in the sense of French capitalisme or German Kapitalismus, with a focus on the symbiosis of wealth and power, including the elimination of competition, rather than merely another term for the market economy.
Long-term improvements in sleep, pain, depression, and fatigue in older adults with comorbid osteoarthritis pain and insomnia
Authors: Vitiello Michael V , Zhu Weiwei , Von Korff Michael , Wellman Robert , Morin Charles M , Yeung Kai , McCurry Susan M
Published: September 2021

In a primary care population of 327 older adults (age 60+) with chronic osteoarthritis (OA) pain and insomnia, we examined the relationship between short-term improvement in sleep or pain and long-term sleep, pain, depression, and fatigue by secondary analyses of randomized controlled trial data. Study participants, regardless of trial arm, were classified as Sleep or Pain Improvers with ≥30% baseline to 2-month reduction on the Insomnia Severity Index or the Brief Pain Inventory, respectively, or Sleep or Pain Non-Improvers. After controlling for trial arm and potential confounders, both Sleep and Pain Improvers showed significant (p < .01) sustained improvements across 12 months compared to respective Non-Improvers for the Insomnia Severity Index (ISI), Pittsburgh Sleep Quality Index, Brief Pain Inventory-short form (total, Interference, and Severity subscales), Patient Health Questionnaire, and Flinders Fatigue Scale. The effect sizes (Cohen’s f2) for the sustained benefits in both Sleep and Pain Improvers compared to their respective Non-Improvers for all variables were small (<0.15) with the exception of medium effect size for sustained reduction in insomnia symptoms for the Sleep Improvers. We conclude that short-term sleep improvements in pain populations with comorbid insomnia precede benefits not only for long-term improvement in sleep but also for reduced pain over the long-term, along with associated improvements in depression and fatigue. Short-term improvements in pain appear to have similar long-term sequelae. Successfully improving sleep in pain populations with comorbid insomnia may have the additional benefits of improving both short- and long-term pain, depression, and fatigue.

Trial Registration: OsteoArthritis and Therapy for Sleep (OATS) NCT02946957: https://clinicaltrials.gov/ct2/show/NCT02946957.
Comparative Internal Market Law: The UK and the EU
Authors: Weatherill Stephen
Published: September 2021

The United Kingdom Internal Market Act 2020 introduces a new field of enquiry for scholars. It allows reflection on the model of an internal market chosen by the United Kingdom to regulate relations between its four constituent elements now that, after Brexit, the authority of the EU’s common rules has come to an end. It allows comparison and contrasts between the UK’s chosen model and the longer established patterns of the EU internal market. It is an invitation to develop a comparative study of the law of internal markets.

The overall structure of the UK internal market envisaged by the 2020 Act is readily compared to that which exists in the EU, but there are also points of contrast. The most significant is that the UK model is less tolerant of regulatory diversity among its constituent elements than applies under EU free movement law. The scope to justify rules that obstruct trade within the UK is less generous than in the EU, with the consequence that the UK’s internal market has a more deregulatory flavour than the EU’s. This model of limited availability to protect local regulatory autonomy over unrestricted intra-UK trade pays little regard to sensitivities in Scotland and Wales, while the position of Northern Ireland, locked into the Protocol attached to the EU–UK Withdrawal Agreement, is different but also fragile. Internal markets possess economic motivations and they are built on legal rules, but they involve political choices and they have political implications. The UK Internal Market Act presents challenges to the stability of the United Kingdom itself.

Accordingly the ambition of this paper is to explain the shape of the UK internal market and to compare and contrast it with the EU’s internal market. It also aims to demonstrate the political sensitivity of the choices that need to be made in designing an internal market against the background competing tensions of unhindered market access, on the one hand, and, on the other, respect for the regulatory autonomy enjoyed by the constituent units.
One-Year Functional, Cognitive, and Psychological Outcomes Following the Use of Extracorporeal Membrane Oxygenation in Coronavirus Disease 2019: A Prospective Study
Authors: Rajajee Venkatakrishna , Fung Christopher Mon-Chee , Seagly Katharine Surella , Park Pauline Kyonsook , Raghavendran Krishnan , Machado-Aranda David Antonio , Scott Jonathan William , Delano Matthew Joseph , Abou El Ela Ashraf Shaaban Abdel Aziz , Haft Jonathan William , Williamson Craig Andrew , McSparron Jakob Israel , Blank Ross , Napolitano Lena Marie
Published: September 2021

Objectives:

To prospectively describe 1-year outcomes, with a focus on functional outcome, cognitive outcome, and the burden of anxiety, depression, and post-traumatic stress disorder, in coronavirus disease 2019 patients managed with extracorporeal membrane oxygenation.

Design:

Prospective case series.

Setting:

Tertiary extracorporeal membrane oxygenation center in the United States.

Patients:

Adult coronavirus disease 2019 acute respiratory distress syndrome patients managed with extracorporeal membrane oxygenation March 1, 2020, to July 31, 2020.

Interventions:

Baseline variables, treatment measures, and short-term outcomes were obtained from the medical record. Survivors were interviewed by telephone, a year following the index intensive care admission. Functional outcome was assessed using the modified Rankin Scale and the World Health Organization Disability Assessment Scale 2.0. Cognitive status was assessed with the 5-minute Montreal Cognitive Assessment. The Hospital Anxiety and Depression Scale was used to screen for anxiety and depression. Screening for post-traumatic stress disorder was performed with the Posttraumatic Stress Disorder Checklist 5 instrument.

Measurements and Main Results:

Twenty-three patients were managed with extracorporeal membrane oxygenation, 14 (61%) survived to hospital discharge. Thirteen (57%) were alive at 1 year. One patient was dependent on mechanical ventilation, another intermittently required supplemental oxygen at 1 year. The median modified Rankin Scale score was 2 (interquartile range, 1–2), median World Health Organization Disability Assessment Scale 2.0 impairment score was 21% (interquartile range, 6–42%). Six of 12 previously employed individuals (50%) had returned to work, and 10 of 12 (83%) were entirely independent in activities of daily living. The median Montreal Cognitive Assessment score was 14 (interquartile range, 13–14). Of 10 patients assessed with Hospital Anxiety and Depression Scale, 4 (40%) screened positive for depression and 6 (60%) for anxiety. Four of 10 (40%) screened positive for post-traumatic stress disorder.

Conclusions:

Functional impairment was common a year following the use of extracorporeal membrane oxygenation in coronavirus disease 2019, although the majority achieved independence in daily living and about half returned to work. Long-term anxiety, depression, and post-traumatic stress disorder were common, but cognitive impairment was not.
Systematic study of precursor effects on structure and oxygen reduction reaction activity of FeNC catalysts
Authors: Theis Pascal , Wallace W. David Z. , Ni Lingmei , Kübler Markus , Schlander Annika , Stark Robert W. , Weidler Natascha , Gallei Markus , Kramm Ulrike I.
Published: September 2021

In this work, the effect of porphyrin loading and template size is varied systematically to study its impact on the oxygen reduction reaction (ORR) activity and selectivity as followed by rotating ring disc electrode experiments in both acidic and alkaline electrolytes. The structural composition and morphology are investigated by
57
Fe Mössbauer spectroscopy, transmission electron microscopy, Raman spectroscopy and Brunauer–Emmett–Teller analysis. It is shown that with decreasing template size, specifically the ORR performance towards fuel cell application gets improved, while at constant area loading of the iron precursor (here expressed in number of porphyrin layers), the iron signature does not change much. Moreover, it is well illustrated that too large area loadings result in the formation of undesired side phases that also cause a decrease in the performance, specifically in acidic electrolyte. Thus, if the impact of morphology is the focus of research it is important to consider the area loading rather than its weight loading. At constant weight loading, beside morphology the structural composition can also change and impact the catalytic performance.

This article is part of the theme issue ‘Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 2)’.
Selective heterogeneous hydrodeoxygenation of acetophenone over monometallic and bimetallic Pt–Co catalyst
Authors: Pino Natalia , Quinchia Jennifer , Gómez Santiago , Espinal Juan F. , Montoya Alejandro , López Diana
Published: September 2021

The hydrodeoxygenation (HDO) of acetophenone was evaluated in liquid phase and gas phase over monometallic Pt/SiO
2
, Co/SiO
2
and bimetallic Pt–Co/SiO
2
catalysts. The influence of reaction time and loading of the catalyst were analysed by following the conversion and products selectivity. Phenylethanol, cyclohexylethanone and cyclohexylethanol are the main products of reaction using the Pt/SiO
2
catalyst. By contrast, ethylbenzene and phenylethanol are the only products formed on the Co/SiO
2
and Pt–Co/SiO
2
catalysts. The bimetallic catalyst is more stable as a function of time and more active towards the HDO process than the monometallic systems. The presence of an organic solvent showed only minor changes in product yields with no effect on the product speciation. Periodic density functional theory analysis indicates a stronger interaction between the carbonyl group of acetophenone with Co than with Pt sites of the mono and bimetallic systems, indicating a key activity of oxophilic sites towards improved selectivity to deoxygenated products.

This article is part of the theme issue ‘Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 2)’.
Identification and initial characterization of a new pair of sibling sRNAs of Neisseria gonorrhoeae involved in type IV pilus biogenesis
Authors: Zachary Marie , Bauer Susanne , Klepsch Maximilian , Wagler Katharina , Hüttel Bruno , Rudel Thomas , Beier Dagmar
Published: September 2021

Non-coding regulatory RNAs mediate post-transcriptional gene expression control by a variety of mechanisms relying mostly on base-pairing interactions with a target mRNA. Though a plethora of putative non-coding regulatory RNAs have been identified by global transcriptome analysis, knowledge about riboregulation in the pathogenic Neisseriae is still limited. Here we report the initial characterization of a pair of sRNAs of

N. gonorrhoeae

, TfpR1 and TfpR2, which exhibit a similar secondary structure and identical single-stranded seed regions, and therefore might be considered as sibling sRNAs. By combination of in silico target prediction and sRNA pulse expression followed by differential RNA sequencing we identified target genes of TfpR1 which are involved in type IV pilus biogenesis and DNA damage repair. We provide evidence that members of the TfpR1 regulon can also be targeted by the sibling TfpR2.
Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase
Authors: Singh Nirbhay , Chauhan Anu , Kumar Ram , Singh Sudheer Kumar
Published: September 2021

Branched-chain amino acids (BCAAs) are essential amino acids, but their biosynthetic pathway is absent in mammals. Ketol-acid reductoisomerase (IlvC) is a BCAA biosynthetic enzyme that is coded by Rv3001c in

Mycobacterium tuberculosis

H37Rv (Mtb-Rv) and MRA_3031 in

M. tuberculosis

H37Ra (Mtb-Ra). IlvCs are essential in Mtb-Rv as well as in

Escherichia coli

. Compared to wild-type and IlvC-complemented Mtb-Ra strains, IlvC knockdown strain showed reduced survival at low pH and under low pH+starvation stress conditions. Further, increased expression of IlvC was observed under low pH and starvation stress conditions. Confirmation of a role for IlvC in pH and starvation stress was achieved by developing

E. coli

BL21(DE3) IlvC knockout, which was defective for growth in M9 minimal medium, but growth could be rescued by isoleucine and valine supplementation. Growth was also restored by complementing with over-expressing constructs of Mtb-Ra and

E. coli

IlvCs. The

E. coli

knockout also had a survival deficit at pH=5.5 and 4.5 and was more susceptible to killing at pH=3.0. The biochemical characterization of Mtb-Ra and

E. coli

IlvCs confirmed that both have NADPH-dependent activity. In conclusion, this study demonstrates the functional complementation of

E. coli

IlvC by Mtb-Ra IlvC and also suggests that IlvC has a role in tolerance to low pH and starvation stress.
Dual-color Fluorescence Cross-Correlation Spectroscopy to study Protein-Protein Interaction and Protein Dynamics in Live Cells
Authors: Hemmen Katherina , Choudhury Susobhan , Friedrich Mike , Balkenhol Johannes , Knote Felix , Lohse Martin , Heinze Katrin G.
Published: September 2021

We present a protocol and workflow to perform live cell dual-color fluorescence crosscorrelation spectroscopy (FCCS) combined with Förster Resonance Energy transfer (FRET) to study membrane receptor dynamics in live cells using modern fluorescence labeling techniques. In dual-color FCCS, where the fluctuations in fluorescence intensity represents the dynamical “fingerprint” of the respective fluorescent biomolecule, we can probe co-diffusion or binding of the receptors. FRET, with its high sensitivity to molecular distances, serves as a well-known “nanoruler” to monitor intramolecular changes. Taken together, conformational changes and key parameters such as local receptor concentrations, and mobility constants become accessible in cellular settings.

Quantitative fluorescence approaches are challenging in cells due to high noise levels and the vulnerable sample itself. We will show how to perform the experiments including the calibration steps. We use dual-color labeled β2-adrenergic receptor (β2AR) labeled (eGFP and SNAPtag-TAMRA). We will guide you step-by-step through the data analysis procedure using open-source software and provide templates that are easy to customize.

Our guideline enables researchers to unravel molecular interactions of biomolecules in live cells in situ with high reliability despite the limited signal-to-noise levels in live cell experiments. The operational window of FRET and particularly FCCS at low concentrations allows quantitative analysis near-physiological conditions.

Link to accompanying video: https://tr240.uni-wuerzburg.de/vippclass/index.php/s/TL8aWmwE9RjGfLE
Condition Medium of Glioblastoma Cell Lines Decreases the Viability of Glioblastoma Cells by Modulating Gene Expression Profile
Authors: Yavuz Mervenur , Akgül Sıddıka , Kaya Egemen , Demircan Turan
Published: September 2021

Grade IV neoplasm of the central nervous system, GBM, is associated with poor prognosis and relatively short overall survival. Due to the current limitations in treatment methods, GBM is characterized as an incurable disease, and research to advance therapeutic options is required. Conditioned medium is commonly used inin-vitrostudies complementary to animal experiments to simulate tumor microenvironment and has the potential to challenge and expand our current understanding of secretome effect on tumor characteristics. This study aimed to investigate the effects of conditioned mediums of GBM cell lines on each other. Conditioned mediums’ cellular and molecular effects were evaluated using commonly employed techniques such as MTT assay, colony formation assay, wound healing assay, EdU labeling-based flow cytometry, and qRT-PCR. Our study demonstrated that conditioned medium harvested from U87 or LN229 cells at 48thh exhibited an anti-growth activity on each other by changing the gene expression pattern. Furthermore, the conditioned medium of LN229 decreased the migration capacity of U87 cells, and the conditioned medium of U87 cells significantly suppressed the LN229 proliferation. We believe that this initial work provides new insights for a better understanding of GBM cell lines’ secretome roles and highlights the necessity of further studies to unveil the secretome content.

Highlights

Conditioned medium harvested from GBM cells at different time points displayed various effects.

Conditioned medium of GBM cell lines harvested at 48thh decreased the viability of each other.

The expression level of anti-and pro-proliferative genes is altered upon condition medium treatment.
Mobile element integration reveals a chromosome dimer resolution system in Legionellales
Authors: Nicholson Beth , Deecker Shayna R. , Ensminger Alexander W.
Published: September 2021

In bacteria, the mechanisms used to repair DNA lesions during genome replication include homologous recombination between sister chromosomes. This can lead to the formation of chromosome dimers if an odd number of crossover events occurs. The concatenated DNA must be resolved before cell separation to ensure genomic stability and cell viability. The broadly conserved dif/Xer system counteracts the formation of dimers by catalyzing one additional crossover event immediately prior to cell separation. While dif/Xer systems have been characterized or predicted in the vast majority of proteobacteria, no homologs to dif or xer have been identified in the order Legionellales. Here we report the discovery of a distinct single-recombinase dif/Xer system in the intracellular pathogen Legionella pneumophila. The dif site was uncovered by our analysis of Legionella mobile element-1 (LME-1), which harbors a dif site-mimic and integrates into the L. pneumophila genome via site-specific recombination. We demonstrate that lpg1867 (herein named xerL) encodes a tyrosine recombinase that is necessary and sufficient for catalyzing recombination at the dif site, and that deletion of dif or xerL causes filamentation along with extracellular and intracellular growth defects. We show that the dif/XerL system is present throughout Legionellales and that Coxiella burnetii XerL and its cognate dif site can functionally substitute for the native system in L. pneumophila. Lastly, we describe an unexpected link between C. burnetii dif/Xer and the maintenance of its virulence plasmids.

Significance Statement

The maintenance of circular chromosomes depends on the ability to resolve aberrant chromosome dimers as they form. In most proteobacteria, broadly conserved Xer recombinases catalyze single crossovers at short, species-specific dif sites located near the replication terminus. Chromosomal dimerization leads to the formation of two copies of dif, leading to rapid site-specific recombination and elimination of the duplicated intervening sequence. The apparent absence of chromosome-dimer resolution mechanisms in Legionellales has been a mystery to date. By studying a phage-like mobile genetic element, LME-1, we have identified a previously unknown single-recombinase dif/Xer system that is not only widespread across Legionellales but whose activity is linked to virulence in two important human pathogens.
Will game-based learning enhance performance?
Authors: Chan Siew H. , Song Qian , Trongmateerut Pailin , Rivera Laurie H.
Published: September 2021

Purpose

Extending the study of Chan et al. (2016), this paper aims to focus on specific aspects of performance (conceptual and factual knowledge) to provide insight into whether computer game attributes designed into Prrinciples Aren’t That Hard (PATH) improve performance.

Design/methodology/approach

A between-subjects experiment is conducted to test the hypotheses. The experimental and control groups are PATH and traditional paper medium, respectively.

Findings

The results reveal that PATH users perform better on the conceptual knowledge questions compared to the traditional paper medium users. No significant difference in performance on the factual knowledge (computational) questions is found between PATH and traditional paper medium users.

Research limitations/implications

This study demonstrates that PATH creates an engaging learning environment, which facilitates the acquisition of conceptual knowledge and improved (conceptual) performance. Research can investigate whether technology may be used to facilitate automation of computational tasks which downplay the importance of computational skills (factual knowledge) and focus on the design of computer game attributes in educational or training programs to enhance conceptual knowledge and (conceptual) performance.

Practical implications

The findings of this study will assist educators and educational technology developers to identify and design motivation-enhancing computer game features to promote remember and understand cognitive processes which improve (conceptual) performance.

Originality/value

Game-based learning serves as the underlying theoretical framework for the design of PATH used in an experimental study to examine the positive effects of motivation-enhancing computer game attributes on remember and understand cognitive processes which facilitate (conceptual) performance. This study also uses separate measures of performance; that is, conceptual and factual knowledge, to provide additional insight into the findings of Chan et al. (2016).
Financial performance assessment of branded and non-branded hotel companies. Analysis of the Portuguese case
Authors: Martins Catarina , Vaz Clara Bento , Alves Jorge Manuel Afonso
Published: September 2021

Purpose

Portugal has been experiencing a continuous growth in tourism activity, with hospitality industry as one of the main tourism sectors. Therefore, the assessment of hotel companies’ performance is very important to assist decision processes. The purpose of this paper is to assess the financial performance (FP) of 570 hotel companies operating hotel units in Portugal in 2017. To explore the question of brand affiliation, a comparison was made between hotel companies with similar stars rating and market orientation. In addition, this paper intends to fill a gap in literature studying the Portuguese reality on the subject of brand affiliation.

Design/methodology/approach

The present study uses a methodology based on data envelopment analysis (DEA) to assess the overall performance for each company, which further decomposed into the within-group performance and the technological gap. The performance of the hotel company is assessed through the aggregation of multiple financial indicators using the composite indicator (CI) derived from the DEA model. A bivariate analysis based on the Tobit regression to test the robustness of brand effect on FP of hotel companies (HC) was also included.

Findings

The empirical results show that branded companies, on average, have significantly better overall FP than non-branded companies. On the one hand, the brand effect tends to improve the within-group FP of HCs and the brand presents a statistically significant positive effect on the FP. On the other hand, the best practices are observed in both branded and non-branded companies.

Practical implications

The results of this study illustrate that, globally, the better FP of the branded companies is because of their individual relative companies’ performance and a better model of operation given by the brand effect. Brand affiliation will generally allow for a better FP and essentially a better profitability for invested equity, a higher return on sales and a higher value added per employee.

Originality/value

The study provides important theoretical and practical contributions that can assist the strategic decision of the HCs in choosing to operate independently or to adopt brand affiliation. Also, it is innovative because the FP of branded and non-branded HCs is measured not using a set of individual financial ratios but through a single CI that aggregates those financial ratios, using a DEA model.
Do you hear my accent? How nonnative English speakers experience conflictual conversations in the workplace
Authors: Kim Regina , Ramirez-Marin Jimena Y. , Tasa Kevin
Published: September 2021

Purpose

The purpose of this paper is to investigate the experiences of nonnative speakers in conflictual situations with native speakers in the workplace. In three studies, the authors examine whether nonnative speakers experience stereotype threat in workplace conflict situations with native speakers, whether stereotype threat is associated with certain conflict managing behaviors (e.g. yielding and avoiding) and the relationship between stereotype threat, satisfaction with conflict outcomes and processes, and objective conflict outcomes.

Design/methodology/approach

Studies 1 and 2 use critical incident recall methodology to examine nonnative speakers’ conflict behaviors and satisfaction with conflict outcomes. In Study 3, data were collected from a face-to-face simulation with a random-assignment design.

Findings

Findings suggest that nonnative speakers indeed experience heightened stereotype threat when interacting with native speakers in conflict situations and the experience of stereotype threat leads to less satisfaction with conflict outcomes, perceptions of goal attainment, as well as worse objective conflict outcomes.

Originality/value

The current study is one of the first studies to document the effects of accent stereotype threat on conflict behaviors and outcomes. More broadly, it contributes to the conflict studies literature by offering new insight into the effects and implications of stereotype threat on workplace conflict behaviors and outcomes.