bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Changes in Fecal Bacterial Microbiota of Dairy Cattle across the Production Line
Authors: Zhao Lei , Li Xunde , Atwill Edward R. , Aly Sharif , Williams Deniece R. , Rossitto Paul , Su Zhengchang
Published: February 2020

Bacteria play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy are still lacking. In this study, we used 16S rRNA sequencing to evaluate the fecal bacterial communities of 90 dairy cattle raised and housed in 12 clearly defined management units on a modern dairy farm. We found that α-diversity differed between several pairs of management units, especially between the hutch calves (management unit 1) and the other units except post weaned heifers (management unit 2). Although β-diversity revealed that most of the samples did not cluster according to their management unit membership except management unit 1, in which the samples grouped and separated from others, we observed three major clusters. Besides the hutch calves (management unit 1), most samples from the other 11 units formed two distinct clusters and the relative abundance of Patescibacteria might be the reason for the separation. Moreover, we identified 212 amplicon sequence variants (ASVs) with relative abundances > 0.1% in more than 10% of the total samples that had significantly different abundances in these units. Furthermore, we found that, as the calves aged, 19 ASVs that were exclusively detected in unit 1, gradually degraded and never reoccurred in other management units. Lastly, we recognized 181 pairs of interactions between 61 ASVs with possibly strong synergistic or antagonistic relationships. These results suggest the enteric microbial communities of dairy cattle housed in different management units are quite dynamic.

IMPORTANCE

Bacterial communities of GIT are crucial for ruminants, such as dairy cattle since they contribute to not only the cattle’s physiology and health but also milk production and food safety that are closely related to human health. Both scientifically and agriculturally, it is necessary to have deep insights into the composition and changes of the bacteria on modern dairy farms. In this study, we provided the profiles of fecal bacterial communities of dairy cattle in each management unit on a modern dairy and described how the enteric microbial communities changed across these management units. The findings have implications for improving animal health, dairy production, farm management, and food safety.
Adult mouse retina explants: an ex vivo window to explore central nervous system diseases
Authors: Schaeffer Julia , Tardy Celine , Albert Floriane , Belin Stephane , Nawabi Homaira
Published: February 2020

When the developing central nervous system (CNS) becomes mature, it loses its ability to regenerate. Therefore, any insult to adult CNS leads to a permanent and irreversible loss of motor and cognitive functions. For a long time, much effort has been deployed to uncover mechanisms of axon regeneration in the CNS. It is now well understood that neurons themselves lose axon regeneration capabilities during development, and also after a lesion or in pathological conditions. Since then, many molecular pathways such as mTOR and JAK/STAT have been associated with axon regeneration. However, no functional recovery has been achieved yet. Today, there is a need not only to identify new molecules implicated in adult CNS axon regeneration, but also to decipher the fine molecular mechanisms associated with regeneration failure. This is critical to make progress in our understanding of neuroprotection and neuroregeneration and for the development of new therapeutic strategies. In this context, it remains particularly challenging to address molecular mechanisms in in vivo models of CNS regeneration. The extensive use of embryonic neurons as in vitro model is a source of bias, as they have the intrinsic competence to grow their axon upon injury, unlike mature neurons. In addition, this type of dissociated neuronal cultures lack a tissue environment to recapitulate properly molecular and cellular events in vitro. Here, we propose to use cultures of adult retina explants to fill this gap. The visual system - which includes the retina and optic nerve - is a gold-standard model to study axon regeneration and degeneration in the mature CNS. Cultures of adult retina explants combine two advantages: they have the simplicity of embryonic neurons cultures and they recapitulate all the aspects of in vivo features in the tissue. Importantly, it is the most appropriate tool to date to isolate molecular and cellular events of axon regeneration and degeneration of the adult CNS in a dish. This ex vivo system allows to set up a large range of experiments to decipher the fine molecular and cellular regulations underlying mature CNS axon growth.
A Pumpless Microfluidic Neonatal Lung Assist Device for Support of Preterm Neonates in Respiratory Distress
Authors: Dabaghi Mohammadhossein , Rochow Niels , Saraei Neda , Fusch Gerhard , Monkman Shelley , Da Kevin , Shahin-Shamsabadi Alireza , Brash John L. , Predescu Dragos , Delaney Kathleen , Fusch Christoph , Selvaganapathy P. Ravi
Published: February 2020

Premature neonates suffer from respiratory morbidity as their lungs are immature and current supportive treatment such as mechanical ventilation or extracorporeal membrane oxygenation (ECMO) cause iatrogenic injuries. A non-invasive and biomimetic concept known as the “artificial placenta” would be beneficial to overcome complications associated with the current respiratory support of preterm infants. Here, a pumpless oxygenator connected to the systemic circulation supports the lung function to relieve respiratory distress. In this paper, we demonstrate the first successful operation of a microfluidic, artificial placenta type neonatal lung assist device (LAD) on a newborn piglet model which is the closest representation of preterm human infants. This LAD has high oxygenation capability in both pure oxygen and room air as the sweep gas. It was able to relieve the respiratory distress that the newborn piglet was put under during experimentation, repeatedly and over significant duration of time. These findings indicate that this LAD has potential application as a biomimetic artificial placenta to support respiratory needs of preterm neonates.
Anopheles stephensias an emerging malaria vector in the Horn of Africa with high susceptibility to EthiopianPlasmodium vivaxandPlasmodium falciparumisolates
Authors: Ashine Temesgen , Teka Hiwot , Esayas Endashaw , Messenger Louisa A. , Chali Wakweya , Meerstein-Kessel Lisette , Walker Thomas , Behaksra Sinknesh Wolde , Lanke Kjerstin , Heutink Roel , Jeffries Claire L. , Mekonnen Daniel Abebe , Hailemeskel Elifaged , Tebeje Surafel K , Tafesse Temesgen , Gashaw Abrham , Tsegaye Tizita , Emiru Tadele , Simon Kigozi , Bogale Eyuel Asemahegn , Yohannes Gedeon , Kedir Soriya , Shumie Girma , Sabir Senya Asfer , Mumba Peter , Dengela Dereje , Kolaczinski Jan H , Wilson Anne , Churcher Thomas S , Chibsa Sheleme , Murphy Matthew , Balkew Meshesha , Irish Seth , Drakeley Chris , Gadisa Endalamaw , Bousema Teun , Tadesse Fitsum G
Published: February 2020

Anopheles stephensi, an efficient Asian malaria vector, recently spread into the Horn of Africa and may increase malaria receptivity in African urban areas. We assessed occurrence, genetic complexity, blood meal source and infection status ofAn. stephensiin Awash Sebat Kilo town, Ethiopia. We used membrane feeding assays to assess competence of localAn. stephensitoP. vivaxandP. falciparumisolates from clinical patients. 75.3% of the examined waterbodies were infested withAn. stephensidevelopmental stages that were genetically closely related to isolates from Djibouti and Pakistan. BothP. vivaxandP. falciparumwere detected in wild-caught adultAn. stephensi. LocalAn. stephensiwas more receptive toP. vivaxcompared to a colony ofAn. arabiensis. We conclude thatAn. stephensiis an established vector in this part of Ethiopia, highly permissive for localP. vivaxandP. falciparumisolates and presents an important new challenge for malaria control.

Summary of the article

An. stephensi, a metropolitan malaria vector that recently expanded to the Horn of African, was highly susceptible to localP. falciparumandP. vivaxisolates from Ethiopia and may increase malariogenic potential of rapidly expanding urban settings in Africa.
Untargeted Metabolomics Shows Alterations in Homocysteine, Lipids and Fatty Acids predicting Memory Decline in Healthy Middle-Aged Individuals
Authors: Hajjar Ihab , Cai Qingpo , Yu Tianwei , Jones Dean P.
Published: February 2020

INTRODUCTION

Some aspects of memory start declining in the fifth decade which may be related to systemic metabolic changes. These changes have not been fully identified. This is the first Metabolome-Wide Association Study of the human plasma for the longitudinal change in memory in healthy adults.

METHODS

Ultra-high resolution mass spectrometry with liquid chromatography was performed on 207 University employees’ plasma.

RESULTS

From 10,201 measured metabolic features, 558 differed between those experiencing change vs no change in memory (False Discovery Rate, FDR< 0.2). Differentially abundant metabolites were observed in lipid and fatty acid metabolism pathways: glycerophospholipid (p=0.0003), fatty acid (p=0.0003) and linoleate (p=0.0003) pathways. Within these pathways, higher homocysteine (OR for memory decline=1.09, FDR=0.19) and lower arachidonic acid (OR=0.97, FDR=0.19), sterol (OR=0.92, FDR=0.02), acetylcholine (OR=0.78, FDR=0.19), carnitine (OR=0.75, FDR=0.19) and linoleic acid (OR=0.74, FDR=0.19) were associated memory decline.

DISCUSSION

Altered systemic lipid and fatty acid are linked with early memory decline in middle-aged individuals.
Post-copulatory behavior of olive baboons (Papio anubis) infected byTreponema pallidum
Authors: Paciência Filipa M. D. , Chuma Idrissa S. , Lipende Iddi F. , Knauf Sascha , Zinner Dietmar
Published: February 2020

In nonhuman primates pathogens are known to exert a profound and pervasive cost on various aspects of their sociality and reproduction. In olive baboons (Papio anubis) at Lake Manyara National Park, genital skin ulcers caused byTreponema pallidumsubsp.pertenuelead to mating avoidance in females and altered mating patterns at a pre-copulatory and copulatory level. Beyond this level, sexual behavior comprises also post-copulatory interactions among the sexual partners. To investigate whether the presence of genital skin ulcers has an impact at the post-copulatory level, we analyzed 517 copulation events of 32 cycling females and 29 males. The occurrence of post-copulatory behaviors (i.e., copulation calls, darting [female rapid withdraw from the male] and post-copulatory grooming) was not altered by the presence of genital skin ulcerations. Similarly to other baboon populations, females of our group were more likely to utter copulation calls after ejaculatory copulation. The likelihood of darting was higher after ejaculatory copulations and with the presence of copulation calls. Post-copulatory grooming was rarely observed but when it occurred, males groomed females for longer periods when females uttered copulation calls during, or preceding mating. Our results indicate that despite the presence of conspicuous genital skin ulcers, the post-copulatory behavior was not affected by the genital health status of the dyad. This suggests that infection cues play a major role before and during mating but do not affect post-copulatory behavior.
Staphylococcal DNA repair is required for infection
Authors: Ha Kam Pou , Clarke Rebecca S. , Kim Gyu-Lee , Brittan Jane L. , Rowley Jessica E. , Mavridou Despoina A. I. , Parker Dane , Clarke Thomas B. , Nobbs Angela H. , Edwards Andrew M.
Published: February 2020

The repair of DNA damage is essential for bacterial viability and contributes to adaptation via increased rates of mutation and recombination. However, the mechanisms by which DNA is damaged and repaired during infection are poorly understood. Using a panel of transposon mutants, we identified therexBAoperon as important for the survival ofStaphylococcus aureusin whole human blood. Mutants lackingrexBwere also attenuated for virulence in murine models of both systemic and skin infections. We then demonstrated that RexAB is a member of the AddAB family of helicase/nuclease complexes responsible for initiating the repair of DNA double strand breaks. Using a fluorescent reporter system, we were able to show that neutrophils cause staphylococcal DNA double strand breaks via the oxidative burst, which are repaired by RexAB, leading to induction of the mutagenic SOS response. We found that RexAB homologues inEnterococcus faecalisandStreptococcus gordoniialso promoted survival of these pathogens in human blood, suggesting that DNA double strand break repair is required for Gram-positive bacteria to survive in host tissues. Together, these data demonstrate that DNA is a target of host immune cells, leading to double-strand breaks, and that repair of this damage by an AddAB-family enzyme enables the survival of Gram-positive pathogens during infection.
The strength and form of natural selection on transcript abundance in the wild
Authors: Ahmad Freed , Debes Paul V. , Nousiainen Ilkka , Kahar Siim , Pukk Lilian , Gross Riho , Ozerov Mikhail , Vasemägi Anti
Published: February 2020

Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. We estimated selection on transcript abundance in cohort of a wild salmonid fish (Salmo trutta) affected by a myxozoan parasite through mark-recapture field sampling and the integration of RNA-seq with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) and subsequent host survival is linked to the upregulation of mitotic cell cycle genes. We also detect a widespread signal of disruptive selection; intermediate transcription levels were frequently associated with reduced host survival. Our results provide insights how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary natural selection driven by climate change and emerging anthropogenic threats.
Plastid gene expression is required for singlet oxygen-induced chloroplast degradation and cell death
Authors: Alamdari Kamran , Fisher Karen E. , Sinson Andrew B. , Chory Joanne , Woodson Jesse D.
Published: February 2020

Chloroplasts constantly experience photo-oxidative stress while performing photosynthesis. This is particularly true under abiotic stresses that lead to the accumulation of reactive oxygen species (ROS). While ROS leads to the oxidation of DNA, proteins, and lipids, it can also act as a signal to induce acclimation through chloroplast degradation, cell death, and nuclear gene expression. Although the mechanisms behind ROS signaling from chloroplasts remain mostly unknown, several genetic systems have been devised in the model plantArabidopsisto understand their signaling properties. One system uses theplastid ferrochelatase two(fc2) mutant that conditionally accumulates the ROS singlet oxygen (1O2) leading to chloroplast degradation and eventually cell death. Here we have mapped three mutations that suppress chloroplast degradation in thefc2mutant and demonstrate that they affect two independent loci (PPR30andmTERF9) encoding chloroplast proteins predicted to be involved in post-transcriptional gene expression. Mutations in either gene were shown to lead to broadly reduced chloroplast gene expression, impaired chloroplast development, and reduced chloroplast stress signaling. In these mutants, however,1O2levels were uncoupled to chloroplast degradation suggesting that PPR30 and mTERF9 are involved in ROS signaling pathways. In the wild type background,ppr30andmTERF9mutants were also observed to be less susceptible to cell death induced by excess light stress. Together these results suggest that plastid gene expression (or the expression of specific plastid genes) is a necessary prerequisite for chloroplasts to activate1O2signaling pathways to induce chloroplast degradation and/or cell death.

Significance summary

Reactive oxygen species accumulate in the chloroplast (photosynthetic plastids) and signal for stress acclimation by inducing chloroplast degradation, cell death, and changes in nuclear gene expression. We have identified two chloroplast-localized proteins involved in gene regulation that are required to transmit these signals, suggesting that proper plastid gene expression and chloroplast development is necessary to activate chloroplast controlled cellular degradation and nuclear gene expression pathways.
HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps
Authors: Dimmick Michael C. , Lee Leo J. , Frey Brendan J.
Published: February 2020

Motivation

Hi-C data has enabled the genome-wide study of chromatin folding and architecture, and has led to important discoveries in the structure and function of chromatin conformation. Here, high resolution data plays a particularly important role as many chromatin substructures such as Topologically Associating Domains (TADs) and chromatin loops cannot be adequately studied with low resolution contact maps. However, the high sequencing costs associated with the generation of high resolution Hi-C data has become an experimental barrier. Data driven machine learning models, which allow low resolution Hi-C data to be computationally enhanced, offer a promising avenue to address this challenge.

Results

By carefully examining the properties of Hi-C maps and integrating various recent advances in deep learning, we developed a Hi-C Super-Resolution (HiCSR) framework capable of accurately recovering the fine details, textures, and substructures found in high resolution contact maps. This was achieved using a novel loss function tailored to the Hi-C enhancement problem which optimizes for an adversarial loss from a Generative Adversarial Network (GAN), a feature reconstruction loss derived from the latent representation of a denoising autoencoder, and a pixel-wise loss. Not only can the resulting framework generate enhanced Hi-C maps more visually similar to the original high resolution maps, it also excels on a suite of reproducibility metrics produced by members of the ENCODE Consortium compared to existing approaches, including HiCPlus, HiCNN, hicGAN and DeepHiC. Finally, we demonstrate that HiCSR is capable of enhancing Hi-C data across sequencing depth, cell types, and species, recovering biologically significant contact domain boundaries.

Availability

We make our implementation available for download at:https://github.com/PSI-Lab/HiCSR

Contact

ljlee@psi.toronto.edu

Supplementary information

Available Online
Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study
Authors: Garg Manik , Couturier Dominique-Laurent , Nsengimana Jérémie , Fonseca Nuno A. , Wongchenko Matthew , Yan Yibing , Lauss Martin , Jönsson Göran B , Newton-Bishop Julia , Parkinson Christine , Middleton Mark R. , Bishop Tim , Corrie Pippa , Adams David J. , Brazma Alvis , Rabbie Roy
Published: February 2020

Purpose

Predicting outcomes after resection of primary melanoma remains crude, primarily based on tumour thickness. We explored gene expression signatures for their ability to better predict outcomes.

Methods

Differential expression analysis of 194 primary melanomas resected from patients who either developed distant metastasis (n=89) or did not (n=105) was performed. We identified 121 metastasis-associated genes that were included in our prognostic signature, “Cam_121”. Several machine learning classification models were trained using nested leave- one-out cross validation (LOOCV) to test the signature’s capacity to predict metastases, as well as regression models to predict survival. The prognostic accuracy was externally validated in two independent datasets.

Results

Cam_121 performed significantly better in predicting distant metastases than any of the models trained with the clinical covariates alone (pAccuracy=4.92×10−3), as well as those trained with two published prognostic signatures. Cam_121 expression score was strongly associated with progression-free survival (HR=1.7, p=3.44×10−6), overall survival (HR=1.73, p=7.71×10−6) and melanoma-specific survival (HR=1.59, p=0.02). Cam_121 expression score also negatively correlated with measures of immune cell infiltration (ρ=−0.73, p<2.2×10−16), with a higher score representing reduced tumour lymphocytic infiltration and a higher absolute 5-year risk of death in stage II melanoma.

Conclusions

The Cam_121 primary melanoma gene expression signature outperformed currently available alternatives in predicting the risk of distant recurrence. The signature confirmed (using unbiased approaches) the central prognostic importance of immune cell infiltration in long-term patient outcomes and could be used to identify stage II melanoma patients at highest risk of metastases and poor survival who might benefit most from adjuvant therapies.

Translational relevance

Predicting outcomes after resection of primary melanoma is currently based on traditional histopathological staging, however survival outcomes within these disease stages varies markedly. Since adjuvant systemic therapies are now being used routinely, accurate prognostic information is needed to better risk stratify patients and avoid unnecessary use of high cost, potentially harmful drugs, as well as to inform future adjuvant strategies. The Cam_121 gene expression signature appears to have this capability and warrants evaluation in prospective clinical trials.
Ecological stoichiometric characteristics of Carbon (C), Nitrogen (N) and Phosphorus (P) in leaf, root, stem, and soil in four wetland plants communities in Shengjin Lake, China
Authors: Dibar Dagne Tafa , Zhang Kun , Yuan Suqiang , Zhang Jinyu , Zhou Zhongze , Ye Xiaoxin
Published: February 2020

Ecological stoichiometric should be incorporated into management and nutrient impacted ecosystems dynamic to understand the status of ecosystems and ecological interaction. The present study focused on ecological stoichiometric characteristics of different macrophyte plants soil, leave, stem and root after the removal of seine fishing since 2000 from Shengjin Lake. For C, N and P analysis from leaves, stems, roots and soil to explore their stoichiometric ratio and deriving environmental forces here four dominant plant communities (Zizania caduciflora, Vallisineria natans, Trapa quadrispinosaandCarex schmidtii) were collected. C, N, P and C: N: P ratio in leafs, stems, roots and soil among the plant communities vary and the studied plant communities had significant effect on the measured variables. There was high C: N inC.schmidtiisoil (7.08±1.504) but not vary significantly (P>0.05), and N: P ratio measured high inV. natans(13.7±4.05) and C: P inT.quadrispinosa soil(81.14±43.88) and showed significant variation (P<0.05) respectively. High leaf C: N and N: P ratio was measured inC. schmidtiiandV. natansrespectively. Nevertheless, high leaf C: P ratio was measured inZ.caduciflora. From the three studied organs leafs C: N, N: P ratio showed high values compared to root and stems. The correlation analysis result showed that, at 0-10cm depth ranges SOC correlated negatively with stem total phosphorus (STP), and RTN (P<0.05) but positively strongly with LTP and LTN (P<0.01) respectively. Soil total nitrogen at 0-10cm strongly positively correlated with LTP (P<0.01) and positively with RN: P and LTC (P<0.05). Soil basic properties such as SMC.BD and pH positively correlated with soil ecological stoichiometric characteristics. Redundancy analysis (RDA) result showed pH and available phosphorus were the potential determinant of soil stoichiometry.
Inflammatory state of lymphatic vessels and miRNA profiles associated with relapse in ovarian cancer patients
Authors: Johnson Sarah C , Chakraborty Sanjukta , Drosou Anastasios , Cunnea Paula , Tzovaras Dimitrios , Nixon Katherine , Zawieja David C , Muthuchamy Mariappan , Fotopoulou Christina , Moore James E
Published: February 2020

Lymphogenic spread is associated with poor prognosis in epithelial ovarian cancer (EOC), yet little is known regarding roles of non-peri-tumoural lymphatic vessels (LVs) outside the tumour microenvironment that may impact relapse. The aim of this feasibility study was to assess whether inflammatory status of the LVs and/or changes in the miRNA profile of the LVs have potential prognostic and predictive value for overall outcome and risk of relapse. Samples of macroscopically normal human lymph LVs (n=10) were isolated from the external iliac vessels draining the pelvic region of patients undergoing debulking surgery. This was followed by quantification of the inflammatory state (low, medium and high) and presence of cancer-infiltration of each LV using immunohistochemistry. LV miRNA expression profiling was also performed, and analysed in the context of high versus low inflammation, and cancer-infiltrated versus non-cancer-infiltrated. Results were correlated with clinical outcome data including relapse with an average follow-up time of 13.3 months. The presence of a high degree of inflammation correlated significantly with patient relapse (p=0.033). Cancer-infiltrated LVs showed a moderate but non-significant association with relapse (p=0.07). Differential miRNA profiles were identified in cancer-infiltrated LVs and those with high versus low inflammation. In particular, several members of the let-7 family were consistently down-regulated in highly inflamed LVs (>1.8-fold, p<0.05) compared to the less inflamed ones. Down-regulation of the let-7 family appears to be associated with inflammation, but whether inflammation contributes to or is an effect of cancer-infiltration requires further investigation.
The Intergenic Small Non-Coding RNAittAis Required for Optimal Infectivity and Tissue Tropism inBorrelia burgdorferi
Authors: Medina-Pérez Diana N. , Wager Beau , Troy Erin , Gao Lihui , Norris Steven J. , Lin Tao , Hu Linden , Hyde Jenny A. , Lybecker Meghan , Skare Jon T.
Published: February 2020

Post-transcriptional regulation via small regulatory RNAs (sRNAs) has been implicated in diverse regulatory processes in bacteria, including virulence. One class of sRNAs, termedtrans-acting sRNAs, can affect the stability and/or the translational efficiency of regulated transcripts. In this study, we utilized a collaborative approach that employed data from infection with theBorrelia burgdorferiTn library, coupled with Tn-seq, together with borrelial sRNA and total RNA transcriptomes, to identify an intergenictrans-acting sRNA, which we designate here asittAforinfectivity-associated andtissue-tropic sRNA locusA. The genetic inactivation ofittAresulted in a significant attenuation in infectivity, with decreased spirochetal load in ear, heart, skin and joint tissues. In addition, theittAmutant did not disseminate to peripheral skin sites or heart tissue, suggesting a role forittAin regulating a tissue-tropic response. RNA-Seq analysis determined that 19 transcripts were differentially expressed in theittAmutant relative to its genetic parent, includingvraA, bba66,ospDandoms28(bba74). Subsequent proteomic analyses also showed a significant decrease of OspD and Oms28 (BBA74) proteins. To our knowledge this is the first documented intergenic sRNA that alters the infectivity potential ofB. burgdorferi.

AUTHOR SUMMARY

Lyme disease is a tick-borne infection mediated by the spirochetal bacterium,Borrelia burgdorferi, that is responsible for greater than 300,000 infections in the United States per year. As such, additional knowledge regarding how this pathogen modulates its regulatory armamentarium is needed to understand howB. burgdorferiestablishes and maintains infection. The identification and characterization of small, non-coding RNA molecules in living systems, designated as sRNAs, has recalibrated how we view post-transcriptional regulation. Recently, over 1,000 sRNAs were identified inB. burgdorferi. Despite the identification of these sRNAs, we do not understand how they affect infectivity orB. burgdorferipathogenesis related outcomes. Here, we characterize theittA B. burgdorferisRNA and show that it is essential for optimal infection using murine experimental infection as our readout. We also track the effect of this sRNA on the transcriptional and proteomic profile as the first step in providing mechanistic insight into how this important sRNA mediates its regulatory effect.
ERECTA family signaling constrainsCLAVATA3andWUSCHELto the center of the shoot apical meristem
Authors: Zhang Liang , DeGennaro Daniel , Lin Guangzhong , Chai Jijie , Shpak Elena D.
Published: February 2020

The shoot apical meristem (SAM) is a reservoir of stem cells that gives rise to all post-embryonic aboveground plant organs. The size of the SAM remains stable over time due to a precise balance of stem cell replenishment versus cell incorporation into organ primordia. The WUSCHEL (WUS)/CLAVATA (CLV) negative feedback loop is central to SAM size regulation. Its correct function depends on accurate spatial expression ofWUSandCLV3. A signaling pathway, consisting of ERECTA family (ERf) receptors and EPIDERMAL PATTERNING FACTOR LIKE (EPFL) ligands, restricts SAM width and promotes leaf initiation. While ERf receptors are expressed throughout the SAM, EPFL ligands are expressed in its periphery. Our genetic analysis demonstrated that ERfs and CLV3 synergistically regulate the size of the SAM, andwusis epistatic toerfs. Furthermore, activation of ERf signaling with exogenous EPFLs resulted in a rapid decrease ofCLV3andWUSexpression. ERf-EPFL signaling inhibits expression ofWUSandCLV3in the periphery of the SAM, confining them to the center. These findings establish the molecular mechanism for stem cell positioning along the radial axis.

Summary statement

ERf signaling restricts the width of the shoot apical meristem, a structure which generates aboveground plant organs, by inhibiting expression of two principal regulators,CLV3andWUS, at its periphery.
Single-molecule sequencing of long DNA molecules allows high contiguityde novogenome assembly for the fungus fly,Sciara coprophila
Authors: Urban John M. , Foulk Michael S. , Bliss Jacob E. , Coleman C. Michelle , Lu Nanyan , Mazloom Reza , Brown Susan J. , Spradling Allan C. , Gerbi Susan A.
Published: February 2020

The lower Dipteran fungus fly,Sciara coprophila, has many unique biological features. For example,Sciaraundergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination inSciarawas the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence forSciara coprophilato take a large step forward in aiding these studies. We approached assembling theSciaragenome using multiple sequencing technologies: PacBio, Oxford Nanopore MinION, and Illumina. To find an optimal assembly using these datasets, we generated 44 Illumina assemblies using 7 short-read assemblers and 50 long-read assemblies of PacBio and MinION sequence data using 6 long-read assemblers. We ranked assemblies using a battery of reference-free metrics, and scaffolded a subset of the highest-ranking assemblies using BioNano Genomics optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. Moreover, we anchored nearly half of theSciaragenome sequence into chromosomes. Finally, we used the signal level of both the PacBio and Oxford Nanopore data to explore the presence or absence of DNA modifications in theSciaragenome since DNA modifications may play a role in imprinting inSciara, as they do in mammals. These data serve as the foundation for future research by the growing community studying the unique features of this emerging model system.
Functional insights from biophysical study of TREM2 interactions with ApoE and Aβ1-42
Authors: Kober Daniel L. , Stuchell-Brereton Melissa D. , Kluender Colin E. , Dean Hunter B. , Strickland Michael R. , Steinberg Deborah F. , Nelson Samantha S. , Baban Berevan , Holtzman David M. , Frieden Carl , Alexander-Brett Jennifer , Roberson Erik D. , Song Yuhua , Brett Tom J.
Published: February 2020

INTRODUCTION

TREM2 is an innate immune receptor expressed on myeloid cells including microglia in the brain. How TREM2 engages different ligands remains poorly understood.

METHODS

We used comprehensive BLI analysis to investigate the TREM2 interactions with ApoE and monomeric amyloid beta (mAβ42).

RESULTS

TREM2 binding did not depend on ApoE lipidation, and there were only slight differences in affinity observed between ApoE isoforms (E4 > E3 > E2). Surprisingly, disease-linked TREM2 variants within a “basic patch” minimally impact ApoE binding. Instead, TREM2 has a unique hydrophobic surface that can bind to ApoE. This direct engagement requires the hinge region of ApoE. TREM2 directly binds mAβ42 and can potently inhibit Aβ42 polymerization, suggesting a potential mechanism for soluble TREM2 (sTREM2) in preventing AD pathogenesis.

DISCUSSION

These findings demonstrate that TREM2 has at least two separate surfaces to engage ligands and uncovers a potential function for sTREM2 in directly inhibiting Aβ polymerization.
Territory-based knowledge management in international marketing processes – the case of “Made in Italy” SMEs
Authors: Festa Giuseppe , Rossi Matteo , Kolte Ashutosh , Situm Mario
Published: February 2020

Purpose

This study aims to analyze the territory as a distinctive factor through which the concept and practice of “Made in Italy” operates. Specifically, the study considers the role of local and sub-national entrepreneurial collaborations that preserve and enhance factors such as history, style and talent as the essence of Italian “quality” and as the pillar of Italian territorial capitalism.

Design/methodology/approach

The research examines this Italian phenomenon by investigating small and medium enterprises (SMEs) that successfully compete abroad (and also in the domestic market) with a “glocal” approach, adopting the entrepreneurial formula of industrial districts.

Findings

The results indicate that international expansion is becoming increasingly more complex (as is every growth/development strategy) but that “glocalism” could represent a potential driver for the success of internationalization strategies. Specifically, for SMEs operating in industrial districts, territorial capitalism could emerge as a unique competitive factor, because it is a component of local structural capital and global reputational capital, as in the case of “Made in Italy.”

Originality/value

In an increasingly globalized market environment, many companies look to foreign markets to maintain and expand competitive advantage and business performance. Once the companies embark on this endeavor, organizations are involved in governing and managing these networks of finance, production and communication and the distribution-related relationships that constitute globalization. The push to engage in international development is currently imperative for SMEs, which need to extend their business engagement beyond conventional local markets and identify and exploit their distinctive competitive advantage to be able to succeed. One possible way of achieving this is the close interaction with the local territories in which these enterprises reside.
Validation of corporate environmental citizenship measurement in Malaysia
Authors: Tay Lee Chin , Tan Fee Yean , Kirana Yahya Khulida , Rasli Amran
Published: February 2020

Purpose

The purpose of this paper is to validate the corporate environmental citizenship measurement originally developed by Banerjee (2002) in the Malaysian setting.

Design/methodology/approach

A systematic sampling technique was used, with a total of 251 responses. The measurement was tested using content validity, convergent validity and discriminant validity.

Findings

The study finds that all four dimensions are highly suited for measuring corporate environmental citizenship in the construction companies in Malaysia.

Research limitations/implications

The study uses a single respondent to report on the organization’s corporate environmental citizenship. The perceptions among the respondents may differ.

Practical implications

Organizations can use the measurement for benchmarking current levels of organizations’ environmental degradation as well as identify which business areas are in need to improve environmental preservation.

Social implications

This study theoretically conceptualized corporate environmental citizenship as a multidimensional construct containing four dimensions.

Originality/value

This study contributes to the body of knowledge by validating corporate environmental citizenship measurement in the Malaysian context as measurement validation studies are scarcely found.
Sustainable fashion: current and future research directions
Authors: Mukendi Amira , Davies Iain , Glozer Sarah , McDonagh Pierre
Published: February 2020

Purpose

The sustainable fashion (SF) literature is fragmented across the management discipline, leaving the path to a SF future unclear. As of yet, there has not been an attempt to bring these insights together or to more generally explore the question of “what is known about SF in the management literature and where could the SF field go from there?”. The purpose of this paper is to bring together the field to identify opportunities for societal impact and further research.

Design/methodology/approach

A systematic literature review was conducted from the first appearances of SF in the management literature in 2000 up to papers published in June 2019, which resulted in 465 included papers.

Findings

The results illustrate that SF research is largely defined by two approaches, namely, pragmatic change and radical change. The findings reveal seven research streams that span across the discipline to explore how organisational and consumer habits can be shaped for the future.

Research limitations/implications

What is known about SF is constantly evolving, therefore, the paper aims to provide a representative sample of the state of SF in management literature to date.

Practical implications

This review provides decision makers with insights that have been synthesised from across the management field.

Originality/value

This review identifies knowledge gaps and informs managerial decision making in the field, particularly through serving as a foundation for further research.
Performance drivers of women-owned microcredit funded enterprises in Tanzania
Authors: Tundui Charles Stephen , Tundui Hawa Petro
Published: February 2020

Purpose

The purpose of this paper is to investigate performance drivers of women-owned businesses that are funded primarily through microcredit. It draws on Storey’s theory of small business growth and family embeddedness axiom to examine the factors that drive the performance of businesses that are funded primarily through microcredit.

Design/methodology/approach

The paper uses a cross-sectional survey that covered 208 women business owners who had access to microcredit. The authors use a logistic regression analysis to model the relationship between independent variables and enterprise performance.

Findings

The paper demonstrates that microcredit plays a significant role in business performance. The credit amount has the most significant influence on the enterprise capital base, whereas the effect on profits is insignificant. Also, owners are more likely to report growth in profits if they possess skills in business management. In addition, younger business owners and necessity entrepreneurs are more likely to report success in their businesses. Other factors that have a significant effect on business performance are product cycle, loan use and family support.

Originality/value

Many women in Tanzania are entering business ownership and depend on microcredit as their primary source of capital for starting and growing their businesses. However, just a few businesses grow into small and medium-sized enterprises. For informed policy decisions, it is important that the factors influencing the performance of funded businesses are known and well understood. This understanding will help the government and development practitioners assist women in achieving business growth rates that could warrant their empowerment and poverty reduction prospects.
Minor sex trafficking of girls with disabilities
Authors: Franchino-Olsen Hannabeth , Silverstein Hannah A. , Kahn Nicole F. , Martin Sandra L.
Published: February 2020

Purpose

The purpose of this paper is to investigate the associations between minor women’ (girls’) disability status and victimization via minor sex trafficking.

Design/methodology/approach

This investigation used data from the National Longitudinal Study of Adolescent to Adult Health, a large, nationally-representative sample of in-school adolescents in the USA that began in 1994. The analysis included bivariate associations between physical disability status or low cognitive ability and minor sex trafficking among female survey respondents (n = 5,430).

Findings

Girls with any disability had a higher prevalence of minor sex trafficking than their peers without disabilities. Odds of minor sex trafficking were significantly higher for those with severe physical disabilities (5.83) and for those with low cognitive abilities (4.86) compared to the odds of their peers without their respective disabilities. Results for girls with mild or moderate physical disabilities were not statistically significant compared to peers without disabilities.

Social implications

These nationally-representative survey data reinforce the trends present in smaller populations and case study research: female adolescents with disabilities are at a heightened risk for sex trafficking. On both a national and global scale, the human rights gaps in policy and practice must be addressed to adequately reach, intervene and protect this vulnerable population.

Originality/value

Research about minor sex trafficking typically relies on small-scale surveys and/or convenience samples. This study used a nationally-representative survey to demonstrate the link between disability status and women’s experiences with minor sex trafficking.
Green human resource management
Authors: Shafaei Azadeh , Nejati Mehran , Mohd Yusoff Yusmani
Published: February 2020

Purpose

The study aimed to provide insights on antecedent and outcome of green HRM at the organisational level and the outcome of green HRM at the individual level. It also sought to examine the mechanism through which green HRM would lead to employees’ positive outcome.

Design/methodology/approach

A quantitative study design using a two-study approach was employed to collect and analyse the data. For study 1, 206 hotels from Malaysia were included in analysis at the organisational level, while in study 2 at the individual level, 508 employees from different sectors provided insights through an online questionnaire. For both studies, partial least squares (PLS–SEM) was used to assess the research model.

Findings

All the proposed hypotheses were supported. Specifically, at the organisational level, organisational environmental culture is positively related to green HRM, and green HRM management positively associates with organisation's environmental performance. At the individual level, green HRM positively influences employees' job satisfaction, and meaningfulness through work is a strong mediator in this relationship.

Originality/value

This study is significant as it contributes to both theory and practice by providing fresh insights on green HRM and its antecedent and outcomes at two levels (organisational and individual) and across two economies (emerging and developed). It also sheds some light on the outcome of green HRM at the employee level which is an area that is still under-researched. By focusing on meaningfulness through work as an important factor, the study contributes to better understanding of green HRM and employees’ positive outcomes.
Agile vs traditional project management approaches
Authors: Zavyalova Elena , Sokolov Dmitri , Lisovskaya Antonina
Published: February 2020

Purpose

Agile project management methods gain increasing attention of practitioners while they often remain neglected by scholarly research. Specifically, there is little known about how performance factors of agile firms differ from those of traditional firms. Scholars argue that these factors often relate to a firm’s human resource management (HRM). This study aims to analyze and compare the HRM architectures in agile and traditional project-based organizations that lead to high firm performance.

Design/methodology/approach

The authors apply fuzzy-set qualitative comparative analysis on data of 154 project-based organizations of diverse professional service industries in Russia.

Findings

This study’s findings suggest that HRM architectures of high-performance agile firms imply a broad use of ability-, motivation- and opportunity-enhancing practices and a high degree of HRM process centralization, while traditional firms adopt more diverse HRM architectures.

Originality/value

Based on this study’s results, the authors stress the importance of ensuring a good fit between a company’s project management approach and HRM architecture. The revealed configurations may also provide guidance for practitioners on designing effective HRM architectures in project-based organizations.
Investigating the relationship between Lean Six Sigma's intangible impacts and organisational innovation climate factors
Authors: Alblooshi Mohamed , Shamsuzzaman Mohammad
Published: February 2020

Purpose

This paper aims to investigate the relationship between the intangible impacts of Lean Six Sigma (LSS) and organisational innovation climate factors and proposes a conceptual model to link them. This paper ultimately aims to extend the range of LSS application by proposing LSS as a tool for fostering organisational innovation.

Design/methodology/approach

The paper followed a qualitative research approach to identify, analyse and categorize the intangible impacts of LSS by reviewing previous literature on its application and conducting in-depth interviews with its experts. Then, a detailed description of organisational innovation climate was provided to highlight its main factors. Finally, a conceptual model was developed to illustrate the relationships among the collected information.

Findings

LSS was found to have many intangible impacts categorized as organisational or individual related. Organisational innovation climate is determined by a number of factors that were found to be positively influenced by many of LSS's intangible impacts. Thus, a number of propositions between LSS's intangible impacts and organisational innovation climate factors were proposed, as illustrated by a conceptual model.

Originality/value

Studying the relationship between LSS and innovation by considering LSS's intangible impacts and linking them to organisational innovation climate factors is a relatively new approach that makes the contribution of this research valuable and significant to academics and professionals.