bluuebunny/crossref_metadata_2025 huggingface dataset:
Short- and mid-term effects of covered stent implantation on extremity findings and heart failure in Parkes Weber syndrome: a case report
Authors: Acar Zeydin , Kırış Abdulkadir , Bektaş Hüseyin , Erden Tuncay
Published: March 2020

Background 

Parkes Weber syndrome (PWS) is a congenital disease characterized by vascular malformations, such as arteriovenous fistulas (AVFs). It frequently presents with overgrowth of a lower limb and high-output heart failure. The main treatment is to close vascular malformations. Surgical excision or endovascular coil insertion was performed in a few patients with AVFs. However, vascular covered stent implantation has not been used for treating PWS.

Case summary 

A 15-year-old male patient with PWS presented to our hospital because of dyspnoea and massive left upper limb swelling. After initial examination and left upper limb angiography, his symptoms and findings were attributed to the presence of high-flow large AVFs despite the presence of many coils previously inserted. We decided to implant a covered stent along the AVFs between the subclavian and axillary arteries. After stent implantation, the patient’s complaints and findings improved during the early term but they relapsed at the 6th month after percutaneous intervention.

Discussion 

Here, we report for the first time the use of covered stent implantation and its short and 6 months results in a patient with PWS. Although initial improvements were noted, the clinical outcome at 6 months after stent implantation was poor. This was probably associated with the presence of widespread subtle AVFs or collateral connections among the existing AVFs. Based on our result, we propose that closure of large AVFs is not useful and more definitive interventions, such as limb amputation may be required earlier.
The membrane lipid metabolism in horticultural products suffering chilling injury
Authors: Liang Shu-min , Kuang Jian-fei , Ji Shu-juan , Chen Qin-fang , Deng Wei , Min Ting , Shan Wei , Chen Jian-ye , Lu Wang-jin
Published: March 2020

Horticultural commodities suffer chilling injury following exposure to extremely low temperatures, which results in visible symptoms and considerable quality loss. Therefore, it is of significance to understand the mechanism of this physiological disorder and to develop effective strategies to control it. Chilling stress causes alteration in structure and function of the plasma membrane, which is assumed to be the primary event in response to cold stress. During this process, the membrane lipid metabolism plays a pivotal role in membrane fluidity and stability. In this review, we summarized the possible roles of membrane lipid metabolism in the development of chilling injury, having the potential for developing effective strategies to alleviate chilling injury in horticultural products under refrigerated storage in practice.
The Imagined Ethno-Racial Border and the Expulsion of Jews from Western Poland, 1939-41*
Authors: Service Hugo
Published: March 2020

Although the ‘Jewish question’ had always figured prominently in Nazi ideology and long-term objectives, the population policy to which Nazi German leaders and officials gave priority in practice in 1939–1941 was the relocation of ethnic-German ‘resettlers’ to annexed western Poland. Christopher Browning and other historians have argued that while in autumn and winter 1939 the Nazi leadership appeared to view the comprehensive removal of Jews from Germany’s ‘incorporated eastern territories’ as a high priority, because they did not prioritize it in practice, it did not happen. This article shows that this interpretation does not fully reflect events. A detailed case study of the expulsion of Jewish residents from east to west within the province of Silesia’s incorporated territory in May–June 1940 demonstrates that for Nazi German elites an ethno-racial boundary ran down the middle of the incorporated territories, north to south, and west of that boundary the comprehensive removal of Jews was prioritized in practice and very nearly realized.
Weighted Gene Coregulation Network Analysis of Promoter DNA Methylation on All-Cause Mortality in Old-Aged Birth Cohorts Finds Modules of High-Risk Associated Biomarkers
Authors: Lund Jesper B , Li Shuxia , Baumbach Jan , Christensen Kaare , Li Weilong , Mohammadnejad Afsaneh , Pattie Alison , Marioni Riccardo E , Deary Ian J , Tan Qihua
Published: March 2020

Overall or all-cause mortality is a key measure of health in a population. Multiple epigenome-wide association studies have been conducted on all-cause mortality with limited significant findings and low replication. To elucidate the coregulated DNA methylation patterns associated with all-cause mortality, we conducted a weighted DNA methylation coregulation network analysis on whole-blood samples of 1,425 older individuals from the Lothian Birth Cohorts of 1921 and 1936. Our network-based analysis defined coregulated DNA methylation patterns in gene promoters into clusters or modules whose correlation with all-cause mortality was assessed by survival analysis. We found two significant modules or gene clusters associated with all-cause mortality in LBC1921 based on their eigengenes; one negatively correlated (p = 8.14E-03, 698 genes) and one positively correlated (p = 4.26E-02, 1,431 genes) with the risk of death. The two modules were replicated in LBC1936 with the same directions of correlation (p = 6.35E-02 and p = 3.64E-02, respectively). Furthermore, the modules revealed 32 genes associated with all-cause mortality (FDR < 0.05) linked to various diseases, including cancer and diabetes. Additionally, we performed pathway analysis and found 22 pathways (FDR < 0.05), including a pathway for taste transduction, which has been shown to be associated with poor prognosis in acutely hospitalized patients, and several pathways were linked to different types of cancer. The results from our network analysis show that DNA methylation of multiple genes could have been coregulated in an association with the overall risk of death. The identified epigenetic markers might help with our understanding of the molecular basis of all-cause mortality and general health.
Neuronal Aquaporin 1 Inhibits Amyloidogenesis by Suppressing the Interaction Between Beta-Secretase and Amyloid Precursor Protein
Authors: Park Jinsu , Madan Meenu , Chigurupati Srinivasulu , Baek Seung Hyun , Cho Yoonsuk , Mughal Mohamed R , Yu Amin , Chan Sic L , Pattisapu Jogi V , Mattson Mark P , Jo Dong-Gyu
Published: March 2020

The accumulation of amyloid-β (Aβ) is a characteristic event in the pathogenesis of Alzheimer’s disease (AD). Aquaporin 1 (AQP1) is a membrane water channel protein belonging to the AQP family. AQP1 levels are elevated in the cerebral cortex during the early stages of AD, but the role of AQP1 in AD pathogenesis is unclear. We first determined the expression and distribution of AQP1 in brain tissue samples of AD patients and two AD mouse models (3xTg-AD and 5xFAD). AQP1 accumulation was observed in vulnerable neurons in the cerebral cortex of AD patients, and in neurons affected by the Aβ or tau pathology in the 3xTg-AD and 5xFAD mice. AQP1 levels increased in neurons as aging progressed in the AD mouse models. Stress stimuli increased AQP1 in primary cortical neurons. In response to cellular stress, AQP1 appeared to translocate to endocytic compartments of β- and γ-secretase activities. Ectopic expression of AQP1 in human neuroblastoma cells overexpressing amyloid precussir protein (APP) with the Swedish mutations reduced β-secretase (BACE1)-mediated cleavage of APP and reduced Aβ production without altering the nonamyloidogenic pathway. Conversely, knockdown of AQP1 enhanced BACE1 activity and Aβ production. Immunoprecipitation experiments showed that AQP1 decreased the association of BACE1 with APP. Analysis of a human database showed that the amount of Aβ decreases as the expression of AQP1 increases. These results suggest that the upregulation of AQP1 is an adaptive response of neurons to stress that reduces Aβ production by inhibiting the binding between BACE1 and APP.
Brain Functional Connectivity Correlates of Response in the 7.5% CO2 Inhalational Model of Generalized Anxiety Disorder: A Pilot Study
Authors: Huneke Nathan T M , Broulidakis M John , Darekar Angela , Baldwin David S , Garner Matthew
Published: March 2020

Background

The 7.5% CO2 inhalational model can be used to explore potential treatments for generalized anxiety disorder. However, it is unknown how inter-individual variability in the functional architecture of negative affective valence systems might relate to anxiogenic response in this model.

Methods

A total of 13 healthy volunteers underwent functional magnetic resonance imaging during a passive emotional face perception task. We explored task-evoked functional connectivity in the potential threat system through generalized psychophysiological interaction analysis. Within 7 days, these participants underwent prolonged 7.5% CO2 inhalation, and results from the generalized psychophysiological interaction analysis were correlated with CO2 outcome measures.

Results

Functional connectivity between ventromedial prefrontal cortex and right amygdala positively correlated with heart rate and subjective anxiety, while connectivity between midcingulate cortex and left amygdala negatively correlated with anxiety during CO2 challenge.

Conclusions

Response to CO2 challenge correlated with task-evoked functional connectivity in the potential threat system. Further studies should assess whether this translates into clinical populations.
Prosecuting the Nexus between Terrorism, Conflict-related Sexual Violence and Trafficking in Human Beings before National Legal Mechanisms
Authors: de Brouwer Anne-Marie , de Volder Eefje , Paulussen Christophe
Published: March 2020

United Nations (UN) Security Council Resolution 2331 (2016) recognizes that ‘acts of sexual and gender-based violence, including when associated to trafficking in persons, are known to be part of the strategic objectives and ideology of certain terrorist groups, used as a tactic of terrorism and an instrument to increase their finances and their power through recruitment and the destruction of communities’. In the same resolution, the Council noted that such trafficking, particularly of women and girls, ‘remains a critical component of the financial flows to certain terrorist groups’ and is ‘used by these groups as a driver for recruitment’. Boko Haram and Al-Shabaab are among the main terrorist groups that have used human trafficking (including for sexual exploitation) and conflict-related sexual violence as tactics of terrorism, or ‘sexual terrorism’. This article will: (i) explain the nexus between these three crimes; (ii) focus on its different manifestations in the context of these terrorist organizations; and (iii) reflect on the possibilities for national criminal prosecution. To assist in the fight against impunity and increase accountability, this article provides suggestions to facilitate the successful prosecution of sexual terrorism in a more survivor-centric way.
Distribution and diversity of squirrels on university and college campuses of the United States and Canada
Authors: Peplinski Joy , Brown Joel S
Published: March 2020

Squirrels on North American college and university campuses have been the subject of much animated conversation in informal venues, but a systematic assessment of their distribution across this habitat type has not been undertaken until now. We collected reports of squirrel species’ presence and absence from faculty experts at 536 campuses in Canada and the continental United States, and found that squirrels are nearly ubiquitous on campuses (95% had at least one species, and 40% had three or more), but that only a select few species are common campus residents. Foremost among these is the eastern gray squirrel (Sciurus carolinensis—on 62% of surveyed campuses), followed by the eastern fox squirrel (Sciurus niger), eastern chipmunk (Tamias striatus), North American red squirrel (Tamiasciurus hudsonicus), and woodchuck (Marmota monax). Eastern gray and fox squirrels partition campuses with one another, both in their shared native/core range and on the West Coast. While these invasive eastern species are present on campuses on the West Coast, notably, contingency analysis did not provide evidence that they are the primary factor discouraging western gray squirrels (Sciurus griseus) from using these habitats. The inventory and analyses presented here can provide a basis for longitudinal studies both within and across campuses and may be productively combined with initiatives that involve students in research.
The assembly of plant–patch networks in Mediterranean alpine grasslands
Authors: Pescador David S , Iriondo José María , Losapio Gianalberto , Escudero Adrián
Published: March 2020

Aims

Harsh environmental conditions in alpine ecosystems shape vegetation structure into patches, where many different plant species cluster and grow together. Yet, which factors are important for the structure and dynamics of such plant–patch networks remains poorly understood. We aim to assess which and how environmental and biotic factors predict the assembly of plant–patch networks along a mountain range.

Methods

We examined the distribution of plant species in more than 5500 vegetation patches in 37 Mediterranean alpine grasslands distributed along a 500 m altitudinal gradient (National Park of Sierra Guadarrama, Spain). We established a plant–patch network for each grassland community and analyzed how nestedness and modularity vary with environmental (altitude, insolation and soil conditions) and biotic factors (number of species per plot, mean patch area and total pasture area).

Important Findings

Plant–patch networks showed consistent, non-random patterns characterized by a nested, but not modular, structure, which suggests that positive associations among co-occurring specialists promote their growth within patches as subsets of a pool with more generalist species. Both nestedness and modularity of plant–patch networks varied among grasslands. Specifically, nestedness decreased with increasing species per plot and increased with mean patch area, while it was independent of environmental variables; modularity increased with increasing pasture area and species per plot. The negative relationship between species per plot and nested patterns may be linked to the restricted number of species that can coexist within the same patch at a given size. Moreover, the positive relationship between patch size and nestedness indicates that the growth of rare plant species within vegetation patches occupied by more abundant species is facilitated in bigger rather than smaller patches. Furthermore, these results indicate that the nested assembly of vegetation patches may be independent of abiotic conditions. These findings suggest that large and unfragmented vegetation patches are fundamental for the maintenance of plant diversity in alpine grasslands. Looking at species distribution at fine spatial scales may shed new light on the biotic processes underlying plant network assembly and provide novel ways for conserving biodiversity.
Preliminary study on radiosensitivity to carbon ions in human breast cancer
Authors: Zhang Qiuning , Kong Yarong , Yang Zhen , Liu Yang , Liu Ruifeng , Geng Yichao , Luo Hongtao , Zhang Hong , Li Hongyan , Feng Shuangwu , Wang Xiaohu
Published: March 2020

The aim of the study was to investigate the various effects of high linear energy transfer (LET) carbon ion (12C6+) and low LET X-ray radiation on MDA-MB-231 and MCF-7 human breast cancer cells and to explore the underlying mechanisms of radiation sensitivity. Cell proliferation, cell colony formation, cell cycle distribution, cell apoptosis and protein expression levels [double-strand break marker γ-H2AX, cell cycle-related protein cyclin B1, apoptosis-related proteins Bax and Bcl-2, and the Akt/mammalian target of rapamycin (mTOR)/ribosomal protein S6 kinase B1 (p70S6K) pathway] were detected after irradiation with carbon ions or X-rays at doses of 0, 2, 4 and 8 Gy. Our results showed that the inhibition of cell proliferation and cell colony formation and the induction of G2/M phase arrest, DNA lesions and cell apoptosis/necrosis elicited by carbon ion irradiation were more potent than the effects elicited by X-ray radiation at the same dose. Simultaneously, compared with X-ray radiation, carbon ion radiation induced a marked increase in Bax and prominent decreases in cyclin B1 and Bcl-2 in a dose-dependent manner. Furthermore, the Akt/mTOR/p70S6K pathway was significantly inhibited by carbon ion radiation in both breast cancer cell lines. These results indicate that carbon ion radiation kills MDA-MB-231 and MCF-7 breast cancer cells more effectively than X-ray radiation, which might result from the inhibition of the Akt/mTOR/p70S6K pathway.
A Porcine Model of Peripheral Nerve Injury Enabling Ultra-Long Regenerative Distances: Surgical Approach, Recovery Kinetics, and Clinical Relevance
Authors: Burrell Justin C , Browne Kevin D , Dutton John L , Laimo Franco A , Das Suradip , Brown Daniel P , Roberts Sanford , Petrov Dmitriy , Ali Zarina , Ledebur Harry C , Rosen Joseph M , Kaplan Hilton M , Wolf John A , Smith Douglas H , Chen H Isaac , Cullen D Kacy
Published: March 2020

BACKGROUND

Millions of Americans experience residual deficits from traumatic peripheral nerve injury (PNI). Despite advancements in surgical technique, repair typically results in poor functional outcomes due to prolonged periods of denervation resulting from long regenerative distances coupled with slow rates of axonal regeneration. Novel surgical solutions require valid preclinical models that adequately replicate the key challenges of clinical PNI.

OBJECTIVE

To develop a preclinical model of PNI in swine that addresses 2 challenging, clinically relevant PNI scenarios: long segmental defects (≥5 cm) and ultra-long regenerative distances (20-27 cm). Thus, we aim to demonstrate that a porcine model of major PNI is suitable as a potential framework to evaluate novel regenerative strategies prior to clinical deployment.

METHODS

A 5-cm-long common peroneal nerve or deep peroneal nerve injury was repaired using a saphenous nerve or sural nerve autograft, respectively. Histological and electrophysiological assessments were performed at 9 to 12 mo post repair to evaluate nerve regeneration and functional recovery. Relevant anatomy, surgical approach, and functional/histological outcomes were characterized for both repair techniques.

RESULTS

Axons regenerated across the repair zone and were identified in the distal stump. Electrophysiological recordings confirmed these findings and suggested regenerating axons reinnervated target muscles.

CONCLUSION

The models presented herein provide opportunities to investigate peripheral nerve regeneration using different nerves tailored for specific mechanisms of interest, such as nerve modality (motor, sensory, and mixed fiber composition), injury length (short/long gap), and total regenerative distance (proximal/distal injury).
Novel Diagnostic Methods and Posttreatment Clinical Phenotypes Among Intracranial Germ Cell Tumors
Authors: Takami Hirokazu , Perry Avital , Graffeo Christopher S , Giannini Caterina , Daniels David J
Published: March 2020

BACKGROUND

Central nervous system (CNS) germ cell tumors (GCT) are rare and complex pediatric neoplasms, the optimal management of which remains an area of active investigation.

OBJECTIVE

To present an updated cohort study, with particular attention to novel diagnostic methods and posttreatment clinical phenotypes.

METHODS

A single-institution cohort study of 80 primary, neurosurgically managed, CNS GCTs was conducted at Mayo Clinic, 1988-2017.

RESULTS

Postchemotherapy resection (eg, second-look surgery) was frequently required (27.0%), especially after adjuvant therapies for nongerminomatous GCTs (NGGCTs; 14 of 28 cases, excluding mature teratoma) and significantly associated with pineal lesions, as compared to neurohypophyseal or bifocal lesions (43.6% vs 5.9% vs 6.7%, P = .004), a finding that retained statistical significance after adjusting for index extent of resection and histology (P = .04). Essentially every NGGCT case underwent at least 1 craniotomy, either on presentation, as second-look surgery, or following local recurrence. Mature teratomatous tissue was highly incident in second-look specimens (84.2%), even among lesions initially diagnosed as germinomas. Pretreatment cerebrospinal fluid (CSF) cell fraction analysis demonstrated an association between single lesions and neutrophil predominance, whereas nongerminomatous GCTs were associated with increased monocyte fractions.

CONCLUSION

CNS GCTs are clinically heterogeneous lesions, resulting in numerous opportunities for improved understanding and clinical management via novel diagnostic and therapeutic protocols. Samples from second-look surgeries for recurrent germinomas frequently demonstrate teratomatous tissue, suggesting possible underdiagnosis of mixed GCTs—particularly among pineal lesions. GCT subtypes demonstrate differential cell fraction distributions on CSF analysis, a novel and perhaps diagnostically helpful finding that requires validation in external cohorts.
A simple score to estimate the likelihood of pseudoprogression vs. recurrence following stereotactic radiosurgery for brain metastases: The Bergen Criteria
Authors: Skeie Bente Sandvei , Enger Per Øyvind , Knisely Jonathan , Pedersen Paal-Henning , Heggdal Jan Ingeman , Eide Geir Egil , Skeie Geir Olve
Published: March 2020

Background

A major challenge in the follow-up of patients treated with stereotactic radiosurgery (SRS) for brain metastases (BM) is to distinguish pseudoprogression (PP) from tumor recurrence (TR). The aim of the study was to develop a clinical risk assessment score.

Methods

Follow-up images of 87 of 97 consecutive patients treated with SRS for 348 BM were analyzed. Of these, 100 (28.7%) BM in 48 (53.9%) patients responded with either TR (n = 53, 15%) or PP (n = 47, 14%). Differences between the 2 groups were analyzed and used to develop a risk assessment score (the Bergen Criteria).

Results

Factors associated with a higher incidence of PP vs. TR were as follows: prior radiation with whole brain radiotherapy or SRS (P = .001), target cover ratio ≥98% (P = .048), BM volume ≤2 cm3 (P = .054), and primary lung cancer vs. other cancer types (P = .084). Based on the presence (0) or absence (1) of these 5 characteristics, the Bergen Criteria was established. A total score <2 points was associated with 100% PP, 2 points with 57% PP and 43% TR, 3 points with 57% TR and 43% PP, whereas >3 points were associated with 84% TR and 16% PP, P < .001.

Conclusion

Based on 5 characteristics at the time of SRS the Bergen Criteria could robustly differentiate between PP vs. TR following SRS. The score is user-friendly and provides a useful tool to guide the decision making whether to retreat or observe at appropriate follow-up intervals.
A possible origin of kilohertz quasi-periodic oscillations in low-mass X-ray binaries
Authors: Kato Shoji , Machida Mami
Published: March 2020

A possible origin of kilohertz quasi-periodic oscillations (QPOs) in low-mass X-ray binaries is proposed. Recent numerical magnetohydrodynamic simulations of accretion disks with turbulent magnetic fields of magneto-rotational instability definitely show the presence of two-armed spiral structure in the quasi-steady state of accretion disks. In such deformed disks, two-armed ($m=2$) c-mode ($n=1$) oscillations are excited by wave–wave resonant instability. Among these excited oscillations, the fundamental in the radial direction ($n_{\rm r}=0$) will be the higher kHz QPO of twin QPOs, and the first overtone ($n_{\rm r}=1$) in the radial direction will be the lower kHz QPO of the twin. A possible cause of the twin high-frequency QPOs in black hole X-ray binaries is also discussed in the final section.
Race and Virulence Analysis of Puccinia triticina in China During 2011 to 2013
Authors: Zhang Lin , Xiao Yu , Gao Ying , Zhao Na , An Yajuan , Yang Wenxiang , Meng Qingfang , Yan Hongfei , Liu Daqun
Published: March 2020

Wheat leaf rust, caused by Puccinia triticina, is a common fungal disease of wheat in China. In order to identify races and determine the individual virulence of isolates in different wheat-growing regions in China, leaf rust samples collected from 18 provinces in 2011 to 2013 were tested on 37 Thatcher near-isogenic lines each carrying a different single leaf rust resistance gene. A total of 158 races were identified. Races THTT (19.5%), THTS (16.9%), PHTT (7.7%), THJS (5.0%), THJT (4.2%), and PHTS (4.0%) were the most predominant races in 2011 to 2013. All of these races were avirulent to resistance genes Lr9 and Lr24. The two most frequent races, THTT and THTS, were widely distributed. The frequencies of the isolates with virulence to Lr1, Lr2c, Lr3, Lr16, Lr26, Lr17, LrB, Lr10, Lr14a, Lr3bg, Lr14b, Lr33, Lr37, and Lr50 exceeded 90%. Frequencies of virulence to Lr2a, Lr3ka, Lr11, Lr30, Lr2b, and Lr32 exceeded 70% but were less than 90%. Frequencies of virulence to Lr18, Lr21, Lr15, Lr23, Lr33+34, Lr36, Lr39, and Lr44 were below 70%, whereas the frequency of virulence to Lr25 was less than 1%. All isolates were avirulent to Lr9, Lr19, Lr24, Lr28, Lr42, Lr29, Lr38, and Lr47. The identified races and individual virulence frequencies provide a basis for selection of effective leaf rust resistance genes for use in breeding programs and can also provide information for the study of race evolution of P. triticina.
Therapeutic delivery from a solid formulation during breastfeeding: a feasibility study
Authors: Maier Theresa , Peirce Paula , Baird Laura , Whitehouse Sophie L. , Slater Nigel K. H. , Beardsall Kathryn
Published: March 2020

Background

Enteral drug and nutrient delivery to breastfed infants depends on the use of oral syringes and liquid formulations. This can pose both practical and emotional challenges to drug delivery.

Objectives

The presented study aimed to explore the potential of using solid formulations for therapeutic delivery during breastfeeding.

Methods

Single centre feasibility study within a tertiary level neonatal unit in the UK, involving twenty-six breastfeeding mother-infant dyads. Vitamin B12 was delivered to infants during breastfeeding from a solid formulation within a commercial silicon nipple shield. Outcomes included the quantitative measurement of change in serum vitamin B12 and a mixed methods assessment of maternal expectations and experiences.

Results

Participants described the surprising ease of ‘drug’ delivery, with no negative impact on breastfeeding behaviour or sensation reported. Vitamin B12 levels rose on average from a baseline of 533 pg/mL (236 - 925 pg/mL) to 1871 pg/mL (610 – 4981 pg/mL) at 6 - 8 hours post-delivery. All mothers expressed their support for this approach, 85% a preference over the use of oral syringes. Reasoning for support related to the reduced medicalisation of this procedure compared to the use of oral syringes, and a desire for choices in relation to their infants’ health.

Conclusions

This study demonstrated that therapeutic delivery from a solid formulation within a nipple shield was feasible and acceptable to mothers and infants.
Genetically encoded biosensors for branched-chain amino acid metabolism to monitor mitochondrial and cytosolic production of isobutanol and isopentanol in yeast
Authors: Zhang Yanfei , Hammer Sarah K. , Carrasco-Lopez Cesar , Garcia Echauri Sergio A. , Avalos José L.
Published: March 2020

Branched-chain amino acid (BCAA) metabolism can be harnessed to produce many valuable chemicals. Among these, isobutanol, which is derived from valine degradation, has received substantial attention due to its promise as an advanced biofuel. WhileSaccharomyces cerevisiaeis the preferred organism for isobutanol production, the lack of isobutanol biosensors in this organism has limited the ability to screen strains at high throughput. Here, we use a transcriptional regulator of BCAA biosynthesis, Leu3p, to develop the first genetically encoded biosensor for isobutanol production in yeast. Small modifications allowed us to redeploy Leu3p in a second biosensor for isopentanol, another BCAA-derived product of interest. Each biosensor is highly specific to isobutanol or isopentanol, respectively, and was used to engineer metabolic enzymes to increase titers. The isobutanol biosensor was additionally employed to isolate high-producing strains, and guide the construction and enhancement of mitochondrial and cytosolic isobutanol biosynthetic pathways, including in combination with optogenetic actuators to enhance metabolic flux. These biosensors promise to accelerate the development of enzymes and strains for branched-chain higher alcohol production, and offer a blueprint to develop biosensors for other products derived from BCAA metabolism.
Integrated analysis of gene correlation reveals disordered relationship between metabolism and immunity in tumor microenvironment
Authors: Chen Zixi , Wei Jinfen , Yuan Yuchen , Cui Ying , Zhang Yanyu , Hu Yumin , Du Hongli
Published: March 2020

Background

Metabolism reprogramming and immune evasion are the most fundamental hallmarks for cancer survival. The complex interactions between metabolism and immune systems in tumors and their microenvironment is complicated. Researching on the correlation changes between metabolic and immune related-genes in normal and tumor tissues would help to reveal these complex interactions.

Methods

In this study, the mRNA profiles across 11 cancer types was obtained from The Cancer Genome Atlas (TCGA). Then, the spearman’s correlation coefficient was calculated between metabolic and immune related-genes for each sample group.

Results

Our results showed that the number of correlated gene pairs was reduced significantly in tumor tissues compared with those of normal tissue, especially in KIRC, KIRP and STAD. Functional enrichment analysis for the universal (the pairs appeared in more than 2 cancer types) and specific (the pairs only in one specific cancer type) gene pairs across cancer types revealed top pathways which appeared in tumor and normal samples, such as phosphatidylinositol signaling system and inositol phosphate metabolism. Thereinto, the pairs in normal tissues missing in tumors may indicate they are important factors affecting immune system, such as, DGKs and PIP4ks. The correlation analysis between immune checkpoint and metabolism genes also showed a reduced correlation in tumor and had the tissue specificity, such as,FUT8was strongly correlated withPDCD1in the HC of STAD and they had a weaker correlation in other normal tissues and tumor types.

Conclusions

Our study provides a novel strategy for investigating interaction of tumor immune and metabolism in microenvironment and offers some key points for exploring new targets including metabolic targets and immunomodulator of immune checkpoints.
The birth of a bacterial tRNA gene by large-scale, tandem duplication events
Authors: Ayan Gökçe B. , Park Hye Jin , Gallie Jenna
Published: March 2020

Organisms differ in the types and numbers of tRNA genes that they carry. While the evolutionary mechanisms behind tRNA gene set evolution have been investigated theoretically and computationally, direct observations of tRNA gene set evolution remain rare. Here, we report the evolution of a tRNA gene set in laboratory populations of the bacteriumPseudomonas fluorescensSBW25. The growth defect caused by deleting the single-copy tRNA gene,serCGA, is rapidly compensated by large-scale (45-290 kb) duplications in the chromosome. Each duplication encompasses a second, compensatory tRNA gene (serTGA) and is associated with a rise in tRNA-Ser(UGA) in the mature tRNA pool. We postulate that tRNA-Ser(CGA) elimination increases the translational demand for tRNA-Ser(UGA), a pressure relieved by increasingserTGAcopy number. This work demonstrates that tRNA gene sets can evolve through duplication of existing tRNA genes, a phenomenon that may contribute to the presence of multiple, identical tRNA gene copies within genomes.
EOMES and IL-10 regulate anti-tumor activity of PD-1+CD4+T-cells in B-cell Non-Hodgkin lymphoma
Authors: Roessner Philipp M. , Cid Laura Llaó , Lupar Ekaterina , Roider Tobias , Bordas Marie , Schifflers Christoph , Gaupel Ann-Christin , Kilpert Fabian , Krötschel Marit , Arnold Sebastian J. , Sellner Leopold , Stilgenbauer Stephan , Dietrich Sascha , Lichter Peter , Izcue Ana , Seiffert Martina
Published: March 2020

The transcription factor Eomesodermin (EOMES) promotes IL-10 production of CD4+T-cells, which has been linked to immunosuppressive and cytotoxic activities. We detected EOMES-expressing CD4+T-cells in lymph node samples of patients with chronic lymphocytic leukemia (CLL) or diffuse large B-cell lymphoma. This was in line with an observed expansion of EOMES-positive CD4+T-cells in leukemic Eµ-TCL1 mice, a well-established model of CLL, and upon adoptive transfer of TCL1 leukemia in mice. Transcriptome and flow cytometry analyses revealed that EOMES does not only drive the transcription of IL-10, but rather controls a unique differentiation program in CD4+T-cells. Moreover, EOMES was necessary for the accumulation of a specific CD4+T-cell subset that expresses IFNγ and IL-10, as well as inhibitory receptors, like PD-1 and LAG3. T-cell transfer studies in leukopenicRag2-/-mice showed that EOMES-deficient CD4+T-cells were inferior in controlling TCL1 leukemia development compared to wildtype T-cells, even though expansion ofEomes-/-CD4+T-cells was observed. We further showed that control of TCL1 leukemia was driven by IL-10 receptor-mediated signals, asIl10rb-deficient CD4+T-cells showed impaired anti-leukemia activity. Altogether, our data suggest that IL-10 producing PD-1+CD4+T-cells contribute to CLL control in an EOMES- and IL-10R-dependent manner.
A novel stimulus paradigm for simultaneous recording of monaural and binaural frequency following response for identification of binaural interaction component
Authors: Bhagavan Srividya Grama , Kalaiah Mohan Kumar
Published: March 2020

The objective of the study was to investigate whether monaural frequency following response (FFR) of right and left ear and binaural FFR could be obtained in the same recording using a novel stimulus presentation paradigm, for the purpose of identification the BIC. Twenty six young adults participated in the study. The FFR was recorded for 220 Hz pure-tone using a novel stimulus paradigm. The pure-tone was presented sequentially to two ears. Initially, the pure-tone was presented to the right ear, then to both ears, and finally to the left ear. The FFR could be elicited from all participants (all three responses: right ear, left ear, and both ears) in the same recording using the novel stimulus presentation paradigm used in the present study. The novel stimulus presentation paradigm used in the present study could be used for obtaining monaural and binaural FFRs in the same recording for identification of BIC.
The Drosophila Amyloid Precursor Protein homologue mediates neuronal survival and neuro-glial interactions
Authors: Kessissoglou Irini A. , Langui Dominique , Hasan Amr , Maral Maral , Dutta Suchetana Bias , Hiesinger P. Robin , Hassan Bassem A.
Published: March 2020

The amyloid precursor protein (APP) is a structurally and functionally conserved transmembrane protein whose physiological role in adult brain function and health is still unclear. Because mutations in APP cause familial Alzheimer’s disease, most research focuses on this aspect of APP biology. We investigated the physiological function of APP in the adult brain using the fruit flyDrosophila melanogaster, which harbors a single APP homologue called APP Like (APPL). Previous studies have provided evidence for the implication of APPL in neuronal wiring and axonal growth through the Wnt signaling pathway. However, like APP, APPL continues to be expressed in all neurons of the adult brain where its functions and their molecular and cellular underpinnings are unknown. We report that APPL loss of function results in the dysregulation of endolysosomal function, in both neurons and glia, with a notable enlargement of early endosomal compartment in neurons followed by neuronal cell death, the accumulation of dead neurons in the brain during a critical period at a young age and subsequent reduction in lifespan. These defects can be rescued by reduction in the levels of the early endosomal regulator Rab5, indicating a causal role of endosomal function for cell death. Finally, we show that the secreted extracellular domain of APPL is taken up by glia, regulates their endosomal morphology and this is necessary and sufficient for the clearance of neuronal debris in an axotomy model. We propose that the APP proteins represent a novel family of neuro-glial signaling proteins required for adult brain homeostasis.
An investigation ofBurkholderiacepacia complex methylomesviaSMRT sequencing and mutant analysis
Authors: Mannweiler Olga , Pinto-Carbó Marta , Lardi Martina , Agnoli Kirsty , Eberl Leo
Published: March 2020

TheBurkholderia cepaciacomplex (Bcc) is a group of 22 closely related opportunistic pathogens which produce a wide range of bioactive secondary metabolites with great biotechnological potential, for example in biocontrol and bioremediation.

This study aimed to investigate methylation in the Bcc by SMRT sequencing, and to determine the impact of restriction-methylation (RM) systems on genome protection and stability and on phenotypic traits. We constructed and analysed a mutant lacking all RM components in the clinical isolateB. cenocepaciaH111. We show that a previously identified essential gene of strain H111,gp51, encoding a methylase within a prophage region, is required for maintaining the bacteriophage in a lysogenic state. We speculate that epigenetic modification of a phage promoter provides a mechanism for a constant, low level of phage production within the bacterial population. We also found that, in addition to bacteriophage induction, methylation was important in biofilm formation, cell shape, motility, siderophore production and membrane vesicle production. Moreover, we found that DNA methylation had a massive effect on the maintenance of the smallest replicon present in this bacterium, which is essential for its virulence.

In silicoinvestigation revealed the presence of two core RM systems, present throughout the Bcc and beyond, suggesting that the acquisition of these RM systems occurred prior to the phylogenetic separation of the Bcc. We used SMRT sequencing of single mutants to experimentally assign theB. cenocepaciaH111 methylases to their cognate motifs. Analysis of the distribution of methylation patterns suggested roles for m6A methylation in replication, since motifs recognised by the core Type III RM system were more abundant at the replication origins of the three H111 replicons, and in regions encoding functions related to cell motility and iron uptake.

Author summary

While nucleotide sequence determines an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, methyltransferases methylate specific motifs to allow discrimination of ‘self’ from ‘non-self’ DNA, e.g. from bacteriophages. Restriction enzymes detect ‘non-self’ methylation patterns and cut foreign DNA. Furthermore, methylation of promoter regions can influence gene expression and hence affect phenotype. In this study, we determined the methylated motifs of four strains from theBurkholderia cepaciacomplex of opportunistic pathogens. Three novel motifs were found, and two that were previously identified in a related species. We deleted the genes encoding the restriction and modification components in a representative strain from among the four sequenced. In this study, methylation is shown to affect various phenotypes, among which maintenance of the lysogenic state of a phage and segregational stability of the smallest megareplicon are most remarkable.
Dual Energy X-ray Absorptiometry (DEXA) as a Longitudinal Outcome Measure of Cancer-Related Muscle Wasting in Mice
Authors: Cole Calvin L. , Robinson Deja , Ye Jian , Mills Bradley , Gerber Scott A. , Beck Christopher A. , Schwarz Edward M. , Linehan David
Published: March 2020

Introduction

Pancreatic ductal adenocarcinoma (PDAC) is notorious for its associated skeletal muscle wasting (SMW) and mortality. Currently, the relationships between PDAC, SMW, and survival are poorly understood. Thus, there is a great need for a faithful small animal model with a quantitative longitudinal outcome measure that recapitulates clinical PDAC, to define SMW onset and assess progression. Therefore, we aimed to validate dual energy X-ray absorptiometry (DEXA) as a longitudinal outcome of lean body mass, and demonstrate its utility to quantify SMW in the KCKO murine model of PDAC.

Methods

In vivo body composition of: 1) untreated mice at 5, 8, 12, 18, and 22 weeks of age (n=4), and 2) a cohort of mice with (n=20) and without PDAC (n=10), was determined via DEXA, and lean mass of the lower hind limbs was predicted via a region of interest analysis by two independent observers. Total body weight was determined. Tibialis anterior (TA) muscles were weighed and processed for histomorphometry immediately post-mortem. Statistical differences between groups were assessed using t-tests and ANOVA. Linear regression models and correlation analysis were used to measure the association between TA and DEXA mass, and reproducibility of DEXA was quantified via the intraclass correlation coefficient (ICC).

Results

Lean mass in growing untreated mice determined by DEXA correlated with TA mass (r2= 0.94; p <0.0001) and body weight (r2= 0.89; p <0.0001). DEXA measurements were highly reproducible between observers (ICC = 0.95; 95% CI: 0.89-0.98). DEXA and TA mass also correlated in the PDAC cohort (r2= 0.76; p <0.0001). Significant SMW in tumor-bearing mice was detected within 38 days of implantation by DEXA, TA mass, and histomorphometry.

Conclusions

DEXA is a longitudinal outcome measure of lower limb lean mass in mice. The KCKO syngeneic model is abona fidemodel of PDAC-associated SMW that can be quantified with longitudinal DEXA.
Envelope Simulation: A New Adaptive Method for Dose Optimization
Authors: Piantadosi Steven , Zhou Guohai
Published: March 2020

We present a flexible and general adaptive experimental design for dose finding clinical trials. This method can be applied in sterotypical settings such as determining a maximum tolerated dose, when the dose response relationship is complex, or when the response is an arbitrary quantitative measure. Our design generalizes dose finding methods such as the continual reassessment method (CRM), modified CRM, and estimation with overdose control (EWOC). Similar to those, our design requires a working mathematical model, which assures efficiency, low bias, and a higher fraction of dose selected near the optimum compared to purely operational designs. Unlike typical model based designs that always employ the same model, our method allows individual dose response models tailored to the circumstance. Simulations are also integral to our design allowing it to account for both known and unknown effects of dose on outcome. This method is applicable to general dose finding problems such as those encountered with modern targeted anti-cancer agents, immunotherapies, and titrations against biomarker outcome measures. The method can also support improvements in the design of the experiment being conducted by providing a platform for concurrent simulations to assess the influence of projected design points. Although we present the design in the context of clinical trials, it is equally applicable to experiments with non-human subjects.
What happens to oak growth and survival when there is both competitionandbrowsing?
Authors: Jensen Anna M. , Petersson Linda K. , Felton Annika , Löf Magnus , Persson Maria
Published: March 2020

Competition from neighboring vegetation and browsing by large herbivores are two of the most important factors affecting the structure and dynamics of temperate forests. While the previous literature has been able to identify individual negative effects from competition or browsing, no one has yet identified and quantified both the individual and the joint effects. Still, when plants face both competition and browsing, it is possible that the combined effect is not simply a sum of the individual negative effects, but perhaps a more complicated situation, where plants perform either better (in case there is also a facilitative effect from the neighboring vegetation) or worse (if the effects amplify each other) than they would if experiencing only one of the two factors. In this paper, we focus on regeneration of oak (Quercus roburL) to study these questions. We analyze a rich data set from a large long-term field experiment conducted at multiple sites in mixed temperate forests in southern Sweden over almost a decade. By the use of four separate treatments on each site – (i) neither competition, nor browsing, (ii) only competition, (iii) only browsing, and (iv) both competition and browsing – we can identify and quantify both the individual and combined effects of competition and browsing on oak growth and survival. We find that both competition and browsing individually affect growth and survival negatively. For growth, browsing has the largest effect, while competition is the larger problem from a survival point of view. When the plant experiences both competition and browsing, the combined, negative, effect is larger than either individual effect for survival, but for growth, the relationship is more complicated, and the surrounding woody vegetation offers at least some protection for the oak, reducing the negative effects from browsing.
Self-labeling of proteins with chemical fluorescent dyes in BY-2 cells and Arabidopsis seedlings
Authors: Iwatate Ryu J. , Yoshinari Akira , Yagi Noriyoshi , Grzybowski Marek , Ogasawara Hiroaki , Kamiya Mako , Komatsu Toru , Taki Masayasu , Yamaguchi Shigehiro , Frommer Wolf B. , Nakamura Masayoshi
Published: March 2020

Abstract

Synthetic chemical fluorescent dyes are promising tools for many applications in biology. SNAP tagging provides a unique opportunity for labeling of specific proteinsin vivowith synthetic dyes for studying for example endocytosis, or super-resolution microscopy. However, despite the potential, chemical dye tagging has not been used effectively in plants. A major drawback was the limited knowledge regarding cell wall and membrane permeability of synthetic dyes. Twenty-six out of 31 synthetic dyes were taken up into BY-2 cells, eight were not taken up and can thus serve for measuring endocytosis. Three of the dyes that were able to enter the cells, SNAP-tag ligands of diethylaminocoumarin, tetramethylrhodamine (TMR) and silicon-rhodamine (SiR) 647 were used to SNAP tag α-tubulin. Successful tagging was verified by live cell imaging and visualization of microtubules arrays in interphase and during mitosis. Fluorescence activation-coupled protein labeling (FAPL) with DRBG-488 was used to observe PIN2 endocytosis and delivery to the vacuole as well as preferential delivery of newly synthesized PIN2 to the newly forming cell plate during mitosis. Together the data demonstrate that specific self-labeling of proteins can be used effectively in plants to study a wide variety to cell biological processes.