bluuebunny/crossref_metadata_2025 huggingface dataset:
Quinocidin, a Cytotoxic Antibiotic with an Unusual 3,4‐Dihydroquinolizinium Ring and Michael Acceptor Reactivity toward Thiols
Authors: Nakagawa Yu , Sawaki Yuki , Kimura Takahiro , Tomura Tomohiko , Igarashi Yasuhiro , Ojika Makoto
Published: November 2017

Cytotoxicity‐guided fractionation of the culture broth of Actinomadura sp. TP‐A0019 led to the isolation of quinocidin (1), a cytotoxic antibiotic with an unusual 3,4‐dihydroquinolizinium ring. The structural assignment was made on the basis of high‐field NMR experiments and chemical synthesis. Comparison of the spectral properties of 1 with those of its synthetic counterparts revealed that 1 is a racemic mixture of two enantiomers, which showed similar cytotoxicity against HeLa‐S3 cells. Nucleophile‐trapping experiments demonstrated that 1 captured 2‐mercaptoethanol and N‐acetyl‐l‐cysteine by means of a Michael addition‐type reaction, but was inert toward 2‐aminoethanol and glycolic acid. Notably, the addition of 1 to thiols proceeded smoothly in neutral aqueous media at room temperature. In view of the thiol‐trapping ability and the unusual structure, 1 provides a unique scaffold for designing drug leads and protein‐labeling probes.
Rhodium‐Catalyzed Asymmetric N−H Functionalization of Quinazolinones with Allenes and Allylic Carbonates: The First Enantioselective Formal Total Synthesis of (−)‐Chaetominine
Authors: Zhou Yirong , Breit Bernhard
Published: November 2017

An unprecedented asymmetric N−H functionalization of quinazolinones with allenes and allylic carbonates was successfully achieved by rhodium catalysis with the assistance of chiral bidentate diphosphine ligands. The high efficiency and practicality of this method was demonstrated by a low catalyst loading of 1 mol % as well as excellent chemo‐, regio‐, and enantioselectivities with broad functional group compatibility. Furthermore, this newly developed strategy was applied as key step in the first enantioselective formal total synthesis of (−)‐chaetominine.
A stereodynamic fluorescent probe for amino acids. Circular dichroism and circularly polarized luminescence analysis
Authors: Carmo dos Santos Nadia Alessandra , Badetti Elena , Licini Giulia , Abbate Sergio , Longhi Giovanna , Zonta Cristiano
Published: November 2017

The use of stereodynamic probes is becoming one of the leading strategies for the fast and effective determination of enantiomeric excess. Recently, we reported a series of novel molecular architectures based on a modified tris(2‐pyridylmethyl)amine complex (TPMA), which are able to amplify the electronic CD, in the case of Zn(II) assemblies and vibrational CD, in the case of Co(II) assemblies. Herein, we report a structural modification of the ligand with the purpose to obtain a fluorescent chiral probe. The study deals with the synthesis of the novel ligand, the formation of the self‐assembly system with amino acids, and the study of the electronic CD and circularly polarized luminescence.
Strategies for Efficient Charge Separation and Transfer in Artificial Photosynthesis of Solar Fuels
Authors: Xu Yuxing , Li Ailong , Yao Tingting , Ma Changtong , Zhang Xianwen , Shah Jafar Hussain , Han Hongxian
Published: November 2017

Converting sunlight to solar fuels by artificial photosynthesis is an innovative science and technology for renewable energy. Light harvesting, photogenerated charge separation and transfer (CST), and catalytic reactions are the three primary steps in the processes involved in the conversion of solar energy to chemical energy (SE‐CE). Among the processes, CST is the key “energy pump and delivery” step in determining the overall solar‐energy conversion efficiency. Efficient CST is always high priority in designing and assembling artificial photosynthesis systems for solar‐fuel production. This Review not only introduces the fundamental strategies for CST but also the combinatory application of these strategies to five types of the most‐investigated semiconductor‐based artificial photosynthesis systems: particulate, Z‐scheme, hybrid, photoelectrochemical, and photovoltaics‐assisted systems. We show that artificial photosynthesis systems with high SE‐CE efficiency can be rationally designed and constructed through combinatory application of these strategies, setting a promising blueprint for the future of solar fuels.
Cytomorphologic features of metastatic endometrioid carcinoma by fine needle aspiration
Authors: Johnson Daniel N. , Barroeta Julieta E. , Antic Tatjana , Lastra Ricardo R.
Published: November 2017

Background

Although metastatic disease is commonly seen in high grade carcinomas of gynecologic origin, it also occurs in low to intermediate grade endometrioid carcinomas (LGEMCAs), and may even be the primary presentation of disease. Tissue confirmation is necessary to guide therapy, but performing biopsies might not always be feasible or practical. In such instances, fine needle aspiration (FNA) is a safe and efficient alternative. No comprehensive series describing the cytomorphologic features of metastatic LGEMCA on FNA samples has been published. This study describes clinical and cytomorphologic features of metastatic LGEMCA diagnosed by FNA.

Methods

The pathology archives at 2 academic institutions were searched for patients with endometrial or ovarian endometrioid carcinoma, with concurrent or subsequent sampling of metastatic sites by FNA.

Results

Twelve cases were identified; all slides were reviewed and cytomorphologic features recorded. Four cases were obtained from metastatic sites as primary presentation of disease, and 8 cases were obtained from metastatic sites in patients with known history of LGEMCA. Metastatic LGEMCAs generate cellular specimens composed of cohesive clusters of cells with areas of gland formation. Consistent cytomorphologic features included nuclear overlapping, low to intermediate nuclear to cytoplasmic ratios, round to elongated nuclear shape, finely vacuolated cytoplasm, mild to moderate nuclear membrane irregularities, squamous metaplasia, and inconspicuous nucleoli. Variability was seen with regards to the presence of necrosis (50% of cases) and mitosis (25% of cases).

Conclusion

The presence of these features on FNA samples should raise concern for an underlying gynecologic malignancy.
Carbon isotopes of C3 herbs correlate with temperature on removing the influence of precipitation across a temperature transect in the agro‐pastoral ecotone of northern China
Authors: Liu Xian‐zhao , Zhang Yong , Li Zhen‐guo , Feng Teng , Su Qing , Song Yan
Published: November 2017

Plant δ13C–temperature (δ‐T) relation has been established in many systems and is often used as paleotemperature transfer function. However, it is still unclear about the exact contributions of temperature variation to plant 13C discrimination because of covariation between temperature and precipitation (aridity), which reduces confidence in reconstruction of paleoclimate. In this study, we measured carbon isotope composition (δ13C) of 173 samples of C3 perennial herbs from 22 sites across a temperature gradient along the 400 mm isohyet in the farming‐pastoral zone of North China. The results showed that precipitation obviously affected the correlations of temperatures and foliar δ13C. After removing the influence of precipitation by analysis of covariance (ANCOVA), a more strongly positive relationship was obtained between site‐mean foliar δ13C and annual mean temperature (AMT), with a regression coefficient of 0.1636‰/°C (p = .0024). For widespread species, Artemisia lavandulaefolia and Artemisia capillaries, the slopes (or coefficients) of foliar δ13C and AMT were significantly steeper (larger) than those of foliar δ13C and AMT where the precipitation influence was not excluded, whereas the δ‐T coefficients of Polygonum persicaria and Leymus chinensis showed little change across the transect after deducting the precipitation effect. Moreover, the positive relationship between temperature and δ13C over the transect could be explained by soil moisture availability related to temperature. Our results may afford new opportunities for investigating the nature of past climate variability.
Reference intervals of trimester‐specific thyroid stimulating hormone and free thyroxine in Chinese women established by experimental and statistical methods
Authors: Han Lican , Zheng Wei , Zhai Yanhong , Xie Xin , Zhang Jingnan , Zhang Shaozu , Zhao Zhen , Cao Zheng
Published: November 2017

Background

As a result of physiological and metabolic changes during pregnancy, thyroid hormones can be affected significantly throughout entire three trimesters. According to the guidelines published by American Thyroid Association in 2017, it is strongly recommended to establish population‐based trimester‐specific and assay method‐specific reference intervals (RIs) using local population.

Methods

A total of 1209 pregnant women without personal or family history of thyroid disease were recruited from July 2015 to April 2017 at Beijing Obstetrics and Gynecology Hospital. Those initially selected patients were further tested for TSH, FT4 and thyroid peroxidase antibody (aTPO), performed on the chemiluminescent platform Siemens ADVIA Centaur® XP. Only patients tested negative for aTPO were included in reference interval establishment. RIs for both TSH and FT4 were determined as 2.5th percentile to 97.5th percentile on the data distribution.

Results

The TSH and FT4 trimester‐specific RIs were as follows: 0.59‐3.54 mIU/L, 11.8‐18.4 pmol/L (n = 188, 1st trimester); 0.80‐4.46 mIU/L, 11.6‐17.4 pmol/L (n = 133, 2nd trimester); 0.72‐4.19 mIU/L, 9.7‐15.1 pmol/L (n = 157, 3rd trimester). The RIs of TSH and FT4 determined by Hoffmann method for first trimester outpatient pregnant women were 0.33‐3.96 mIU/L (n = 9924) and 11.7‐17.5 pmol/L (n = 10039), respectively.

Conclusion

Trimester‐specific thyroid function tests RIs are distinct from those provided by assay manufacturers. The RIs determined by direct sampling and Hoffmann indirect calculation showed no statistical difference.
The radial forearm free flap as a “vascular bridge” for secondary microsurgical head and neck reconstruction in a vessel‐depleted neck
Authors: Ciudad Pedro , Agko Mouchammed , Date Shivprasad , Chang Wei‐Ling , Manrique Oscar J. , Huang Tony C. T. , Lo Torto Federico , Trignano Emilio , Chen Hung‐Chi
Published: November 2017

Background

In a vessel‐depleted neck, distant recipient sites may be the only option for secondary free flap reconstruction. While interposition vein grafts and arteriovenous loops can bridge the gap between the recipient and donor pedicle, they are not without risks. In these scenarios, we examinate the reliablity of a radial forearm free flap (RFFF) as an alternative vascular conduit.

Patients and methods

A retrospective review of cases between March 2005 and May 2016 was performed. Demographic data, prior surgical history, intraoperative details and outcomes were recorded. A total of ten patients, eight male and two female, with a mean age of 54.2 years (range, 39–74) were identified. The RFFF was initially anastomosed to either the thoracoacromial (n = 6) or internal mammary vessels (n = 4) and subsequently served as the recipient pedicle for the second “main” flap, an anterolateral thigh (n = 4), jejunum (n = 3) or fibula flap (n = 3).

Results

The average RFFF dimensions were 13.8 cm by 5.8 cm. All twenty flaps, ten RFFF and ten "main' flaps survived completely with only one case of minimal epidermal loss. One patient with esophageal reconstruction with jejunum developed a fistula that required closure with a local falp. At a mean follow‐up of 18.4 months (range 8–29), the reconstructive goals had been achieved in all cases.

Conclusions

The RFFF serves as a reliable “vascular bridge” that extends the reach of distant recipient sites to free flaps in secondary head and neck reconstruction.
Technical Note: Parallel implementation of the EGSnrc Monte Carlo simulation of ionizing radiation transport using OpenMP
Authors: Doerner Edgardo , Caprile Paola
Published: November 2017

Purpose

To present the implementation of a new option for parallel processing of the EGSnrc Monte Carlo system using the OpenMP API, as an alternative to the provided method based on the use of a batch queuing system (BQS).

Methods

The parallel solution presented, called OMP_EGS, makes use of OpenMP features to control the workload distribution between the compute units. These features were inserted into the original EGSnrc source code through properly defined macros. In order to validate the platform, the possibility of producing results in exact agreement with the serial implementation was assessed. The performance of OMP_EGS was evaluated against the BQS method, in terms of parallel speedup and efficiency.

Results

As the OpenMP features can be activated or deactivated depending on the compilation options, the implementation of the platform allowed the direct recovery of the original serial implementation. The validation tests showed that OMP_EGS was able to reproduce the exact same results as the serial implementation. The performance and scalability tests showed that OMP_EGS is a better alternative than the EGSnrc BQS parallel implementation, both in terms of runtime and parallel efficiency.

Conclusions

The presented solution has several advantages over the BQS‐based parallel implementation available for the EGSnrc system. One of the main advantages is that, in contrast to the BQS alternative, it can be implemented using different compilers and operative systems, which turns it into a compact and portable solution that can be used on a wide range of working environments. It does not introduce artifacts on the simulated distributions, as it only handles the distribution of work among the available computing resources and it proved to have a better performance.
Bay‐annulated indigo based near‐infrared sensitive polymer for organic solar cells
Authors: Zhu Jingshuai , Li Tengfei , Shi Keli , Wang Jiayu , Lin Yuze , Yu Gui , Zhan Xiaowei
Published: November 2017

A new conjugated polymer (PBAIIDTT) based on bay‐annulated indigo and indacenodithieno[3,2‐b]thiophene was designed, synthesized, and characterized. PBAIIDTT shows strong absorption in 400–500 and 600–800 nm, and its HOMO and LUMO energy levels are −5.45 eV and −3.65 eV, respectively. In organic field‐effect transistors, the polymer exhibits a relatively high hole mobility of 0.39 cm2 V−1 s−1. PBAIIDTT was added to poly(3‐hexylthiophene) (P3HT) and phenyl‐C61‐butyric acid methyl ester (PC61BM) based organic solar cells. Ternary blend solar cells with 10% PBAIIDTT show an increased short circuit current density due to the broadened photocurrent generated in the near‐infrared region, and a power conversion efficiency of 3.78%, which is higher than that of the P3HT:PC61BM binary control devices (3.33%). © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018, 56, 213–220
Tribological evaluation of environmentally friendly ionic liquids derived from renewable biomaterials
Authors: Jiang Cheng , Li Weimin , Nian Jingyan , Lou Wenjing , Wang Xiaobo
Published: November 2017

Unlike most of the conventional ionic liquids (ILs) derived from non-renewable resources, five environmentally friendly ILs ([Ch][AA] ILs) derived from amino acids (AAs) and choline (Ch) were synthesized using biomaterials by a simple, green route: acid–base reaction of Ch and AAs. The thermal and corrosion properties, as well as viscosity, of the prepared ILs were examined. The results revealed that the anion structure of ILs plays a dominant role in their thermal and viscosity behavior. These ILs exhibited less corrosion toward copper, related to their halogen-, sulfur-, and phosphorus-free characteristics. The tribological behavior of the synthesized ILs was examined using a Schwingungs Reibung und Verschleiss tester, and the results indicated that these ILs exhibit good friction-reducing and anti-wear properties as lubricants for steel/steel contact. Results from energy-dispersive spectroscopy and X-ray photoelectron spectroscopy indicated that the good tribological properties of [Ch][AA] ILs are related to the formation of a physically adsorbed film on the metal surface during friction.
Civic media literacy as 21st century source work: Future social studies teachers examine web sources about climate change
Authors: Damico James S. , Panos Alexandra
Published: November 2017

Civic media literacy entails understanding complex topics and events that are increasingly mediated by digital sources of information and where it can be challenging to evaluate the reliability merits of these sources. The goal of this study was to discern the ways undergraduate preservice social studies teachers with different climate change beliefs read and evaluated the reliability of four diverse Web sources about the complex socioscientific topic of climate change. Findings highlight clear alignment between most participants with climate change beliefs at either end of a beliefs continuum with less alignment for participants with climate change beliefs toward the middle of a continuum. Findings also point to the benefits of whole group deliberation to help participants more critically evaluate a Web source that opposed the scientific consensus about climate change. In an age of “alternative facts,” this study points to the importance of students and educators having opportunities to evaluate, discuss, and determine the credibility of a range of online sources.
What Precursors Foretold Greenland’s Recent 100-Meter Tsunami?
Authors: Underwood Emily
Published: November 2017

Slippage began hours before a landslide-driven tsunami destroyed a village in northwestern Greenland.
Up-regulation of long non-coding RNA SNHG20 promotes ovarian cancer progression via Wnt/β-catenin signaling
Authors: He Shanyang , Zhao Yunhe , Wang Xiaoping , Deng Yalan , Wan Zhiyong , Yao Shuzhong , Shen Hongwei
Published: November 2017

Long non-coding RNA small nucleolar RNA host gene 20 (SNHG20) has been demonstrated to play crucial regulatory roles in many types of cancer. However, the biological function of long ncRNA (lncRNA) SNHG20 in ovarian cancer is still unclear. In the present study, we found that lncRNA SNHG20 was significantly increased in ovarian cancer. In addition, lncRNA SNHG20 knockdown suppressed the ovarian cancer progression, whereas overexpression of SNHG20 showed the opposite effects. Moreover, our results also revealed that lncRNA SNHG20 knockdown inhibited Wnt/β-catenin signaling activity by suppressing β-catenin expression and reversing the downstream target gene expression. Taken together, lncRNA SNHG20 plays an pivotal role in ovarian cancer progression by regulating Wnt/β-catenin signaling.
Relaxin contributes to the regulation of arterial pressure in adult female mice
Authors: Mirabito Colafella Katrina M. , Samuel Chrishan S. , Denton Kate M.
Published: November 2017

Relaxin is increasingly being recognized as a potent vasodilatory and antifibrotic hormone. Given that relaxin is present in the circulation during the luteal phase of the menstrual cycle and during pregnancy, when arterial pressure is lowest in women, relaxin may contribute to the relative cardiovascular protection observed in premenopausal women as compared with age-matched men and postmenopausal women. In the present study, we investigated the contribution of relaxin to the normal regulation of arterial pressure in adult female and male mice and during pregnancy. Mean arterial pressure (MAP) was measured via radiotelemetry in 14-week-old male and female wild-type (WT; C67BL/6xSv129) and relaxin knockout (KO) mice. Thereafter, female mice were time-mated with a (non-telemetered) male of the same genotype and MAP was measured throughout gestation. Basal MAP was ∼10 mmHg lower in WT females than males (P<0.05). Relaxin deficiency increased basal MAP in females (P<0.05 vs WT female), but not males. As expected, MAP decreased during gestation in WT mice. Conversely, in relaxin KO mice, arterial pressure increased during mid and late gestation (P<0.05 as compared with WT). Moreover, relaxin deficiency impaired gestational weight gain and reduced litter size. This is the first study to (i) demonstrate that relaxin contributes to the sexual dimorphism of arterial pressure in mice and (ii) document the changes in the arterial pressure profile of pregnant relaxin KO mice. Understanding the mechanisms that underlie the regulation of arterial pressure in premenopausal females may uncover new strategies to treat hypertension in women (non-pregnant and pregnant) and men.
Mesenchymal stromal cells improve human islet function through released products and extracellular matrix
Authors: Arzouni Ahmed A. , Vargas-Seymour Andreia , Rackham Chloe L. , Dhadda Paramjeet , Huang Guo-Cai , Choudhary Pratik , Nardi Nance , King Aileen J.F. , Jones Peter M.
Published: November 2017

Aims: The aims of the present study were (i) to determine whether the reported beneficial effects of mesenchymal stromal cells (MSCs) on mouse islet function extend to clinically relevant human tissues (islets and MSCs), enabling translation into improved protocols for clinical human islet transplantation; and (ii) to identify possible mechanisms through which human MSCs influence human islet function.

Materials and methods: Human islets were co-cultured with human adipose tissue-derived MSCs (hASCs) or pre-treated with its products – extracellular matrix (ECM) and annexin A1 (ANXA1). Mouse islets were pre-treated with mouse MSC-derived ECM. Islet insulin secretory function was assessed in vitro by radioimmunoassay. Quantitative RT-PCR was used to screen human adipMSCs for potential ligands of human islet G-protein-coupled receptors.

Results: We show that co-culture with hASCs improves human islet secretory function in vitro, as measured by glucose-stimulated insulin secretion, confirming previous reports using rodent tissues. Furthermore, we demonstrate that these beneficial effects on islet function can be partly attributed to the MSC-derived products ECM and ANXA1.

Conclusions: Our results suggest that hASCs have the potential to improve the quality of human islets isolated for transplantation therapy of Type 1 diabetes. Furthermore, it may be possible to achieve improvements in human islet quality in a cell-free culture system by using the MSC-derived products ANXA1 and ECM.
Manipulation of sensory input can improve stretching outcomes
Authors: Capobianco Robyn A. , Almuklass Awad M. , Enoka Roger M.
Published: November 2017

The primary purpose of our study was to assess the influence of modulating sensory input with either transcutaneous electrical nerve stimulation (TENS) or self‐massage with therapy balls on the maximal range of motion (ROM) about the ankle joint when stretching the calf muscles. We also investigated the influence of these two conditions on the force capacity and force control of plantar flexor muscles. Twenty healthy adults (25 ± 3 yr) performed three sessions of ankle plantar flexor stretching (three stretches of 30 s each): stretching alone (SS), stretching with concurrent TENS (TENS), and stretching after self‐massage using therapy balls (SM). TENS was applied for 60 s prior to and during each stretch, and SM was performed for 60 s prior to each of the three stretches. Maximal voluntary contraction (MVC) torque and force steadiness at 20% MVC were recorded before and at 15 min after the final stretch. Ankle dorsiflexion ROM was assessed before, after, and at 5, 10, and 15 min after the last stretch. The increase in ROM was greater after SM (24%) than after SS (13%) and TENS (9%; p < .001). Maximal discomfort level (0–10 VAS) during stretching was similar for all conditions. MVC torque increased after SM only (p < .001, Cohen's D = 1.5): SM, 16%; SS, –1%; TENS, –3%. Force steadiness did not change. The sensory fibres that contribute to stretch tolerance were engaged by self‐massage but not by TENS, resulting in greater increases in flexibility and MVC torque after self‐massage.
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
Authors: Shin Sunguk , Lee Hanna , Son Hyeonju , Paik Soonmyung , Kim Sangwoo
Published: November 2017

Ion Torrent sequencing is one of the most frequently used platforms in healthcare research and industry. Despite many advantages, platform-specific artifacts complicate efficient separation of true variants from errors, especially in variants with lower allele frequencies (<15%). Here, we developed a multi-step filtering toolbox AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity.

Availability and implementation

The program with a detailed manual is available at https://sourceforge.net/projects/airvf/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Additive effects of pCO2 and temperature on respiration rates of the Antarctic pteropod Limacina helicina antarctica
Authors: Hoshijima Umihiko , Wong Juliet M , Hofmann Gretchen E
Published: November 2017

The Antarctic pteropod, Limacina helicina antarctica, is a dominant member of the zooplankton in the Ross Sea and supports the vast diversity of marine megafauna that designates this region as an internationally protected area. Here, we observed the response of respiration rate to abiotic stressors associated with global change—environmentally relevant temperature treatments (−0.8°C, 4°C) and pH treatments reflecting current-day and future modeled extremes (8.2, 7.95 and 7.7 pH at −0.8°C; 8.11, 7.95 and 7.7 pH at 4°C). Sampling repeatedly over a 14-day period in laboratory experiments and using microplate respirometry techniques, we found that the metabolic rate of juvenile pteropods increased in response to low-pH exposure (pH 7.7) at −0.8°C, a near-ambient temperature. Similarly, metabolic rate increased when pteropods were exposed simultaneously to multiple stressors: lowered pH conditions (pH 7.7) and a high temperature (4°C). Overall, the results showed that pCO2 and temperature interact additively to affect metabolic rates in pteropods. Furthermore, we found that L. h. antarctica can tolerate acute exposure to temperatures far beyond its maximal habitat temperature. Overall, L. h. antarctica appears to be susceptible to pH and temperature stress, two abiotic stressors which are expected to be especially deleterious for ectothermic marine metazoans in polar seas.
Arabidopsis HIPP27 is a host susceptibility gene for the beet cyst nematode Heterodera schachtii
Authors: Radakovic Zoran S. , Anjam Muhammad Shahzad , Escobar Elizabeth , Chopra Divykriti , Cabrera Javier , Silva Ana Cláudia , Escobar Carolina , Sobczak Miroslaw , Grundler Florian M. W. , Siddique Shahid
Published: November 2017

Sedentary plant-parasitic cyst nematodes are obligate biotrophs that infect the roots of their host plant. Their parasitism is based on modification of root cells to form a hypermetabolic syncytium from which the nematodes draw their nutrients. The aim of this study was to identify nematode susceptibility genes in Arabidopsis thaliana and to characterize their roles in supporting the parasitism of Heterodera schachtii. By selecting genes that were most strongly upregulated in response to cyst nematode infection, we identified HIPP27 (HEAVY METAL-ASSOCIATED ISOPRENYLATED PLANT PROTEIN 27) as a host susceptibility factor required for beet cyst nematode infection and development. Detailed expression analysis revealed that HIPP27 is a cytoplasmic protein and that HIPP27 is strongly expressed in leaves, young roots and nematode-induced syncytia. Loss-of-function Arabidopsis hipp27 mutants exhibited severely reduced susceptibility to H. schachtii and abnormal starch accumulation in syncytial and peridermal plastids. Our results suggest that HIPP27 is a susceptibility gene in Arabidopsis whose loss-of-function reduces plant susceptibility to cyst nematode infection without increasing susceptibility to other pathogens or negatively affecting plant phenotype.
Population adaptation in efficient balanced networks
Authors: Gutierrez Gabrielle J. , Denève Sophie
Published: November 2017

Adaptation is a key component of efficient coding in sensory neurons. However, it remains unclear how neurons can provide a stable representation of external stimuli given their history-dependent responses. Here we show that a stable representation is maintained if efficiency is optimized by a population of neurons rather than by neurons individually. We show that spike-frequency adaptation and E/I balanced recurrent connectivity emerge as solutions to a global cost-accuracy tradeoff. The network will re-distribute sensory responses from highly excitable neurons to less excitable neurons as the cost of neural activity increases. This does not change the representation at the population level, despite causing dynamic changes in individual neurons. By applying this framework to an orientation coding network, we reconcile neural and behavioral findings. Our approach underscores the common mechanisms behind the diversity of neural adaptation and its role in producing a reliable representation of the stimulus while minimizing metabolic cost.
Molecular mechanism of the dual regulation of bacterial iron sulfur cluster biogenesis by CyaY and IscX
Authors: Adinolfi Salvatore , Puglisi Rita , Crack Jason C. , Iannuzzi Clara , Dal Piaz Fabrizio , Konarev Petr V. , Svergun Dmitri I. , Martin Stephen , Le Brun Nick E. , Pastore Annalisa
Published: November 2017

IscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialised and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest that iron-sulfur cluster assembly is an exquisite example of an enzymatic process which requires a double regulation under the control of iron as the effector.
The ventral disc is a flexible microtubule organelle that depends on domed ultrastructure for functional attachment ofGiardia lamblia
Authors: Nosala Christopher , Dawson Scott C.
Published: November 2017

The parasiteGiardia lambliainteracts with its host by directly attaching the lumen of the small intestine. Attachment is mediated by a cytoskeletal structure termed the ventral disc and proceeds in four distinct stages: skimming, seal formation, cell body contacts, and bare area contacts. The precise mechanism of disc-mediated attachment is unclear and attachment models rely heavily on whether or not the ventral disc is a dynamic structure. We sought to investigate the second stage of attachment in which a seal is formed beneath the ventral disc. Three-dimensional, live imaging ofGiardiaexpressing specific ventral disc markers to the lateral crest, ventral groove, and disc body indicate dynamic movement in all of these regions. We observe seal formation by the lateral crest and determine that movement of the ventral groove region aids lateral crest seal formation. We also report the discovery of a new protein that is necessary for ventral disc formation and functional attachment (DAP_7268). Lastly, we observed that attachment largely depends on ventral disc ultrastructure as flattened discs display hindered attachment proficiency whether or not they retain the ability to form a seal. We propose a synthesized mechanism for attachment that includes flagellar hydrodynamic flow to help generate suction as well as disc conformational dynamics to aid in both hydrodynamic flow and the maintenance of negative pressure.
Molecular genetic diversity of donkey (Equus asinus) in South Korea
Authors: Yun Sungwook , Cho Giljae
Published: November 2017

The research on domestic donkey has little information and criteria comparing to other livestock, companion animal in South Korea. We analyzed genetic database of domestic donkey using microsatellite marker to clarify domestic donkey identification and paternity test. It is the first microsatellite marker analysis on domestic donkey in South Korea. We studied 179 horse samples from 50 Thoroughbred, 50 Jeju Halla horse, including 79 donkeys then analyzed 15 microsatellite marker (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3 and VHL20). We observed genetic diversity from biostatic analysis of them.

The number of alleles on total average is 6.08 observed from 1 (ASB17), 2 (HMS1) to 14 (AHT5). The observed heterozygosity (OHet) is from 0.0000 (ASB17, HMS1) to 0.8608 (ASB23) which is mean value of 0.4861, the expected heterozygosity (EHet) is from 0.0000 (CA425) to 0.9104 (AHT5) with mean value of 0.5915, and the Polymorphism Information Content (PIC) on each group of microsatellite marker is from 0.0000 (ASB17) to 0.8968 (AHT5) observed as a mean value of 0.5374. Among 15 markers AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, LEX3 is observed above 5.000.

The results on 15 microsatellite marker analysis of 3 horse groups is that the donkey had 0.5915 EHet, 0.4861 OHet on average, Thoroughbred had 0.6721 EHet, 0.6587 OHet on average, and the Jeju halla horse had 0.7898 EHet, 0.7093 OHet on average observed. Furthermore the mean alleles value is observed as 6.08, 4.83, 8.00 in donkey, Thoroughbred, Jeju halla horse breed in each.
Multi-state design of kinetically-controlled RNA aptamer ribosensors
Authors: Burke Cassandra R. , Sparkman-Yager David , Carothers James M.
Published: November 2017

Metabolite-responsive RNA regulators with kinetically-controlled responses are widespread in nature. By comparison, very limited success has been achieved creating kinetic control mechanisms for synthetic RNA aptamer devices. Here, we show that kinetically-controlled RNA aptamer ribosensors can be engineered using a novel approach for multi-state, co-transcriptional folding design. The design approach was developed through investigation of 29 candidatep-aminophenylalanine-responsive ribosensors. We show that ribosensors can be transcribedin situand used to analyze metabolic production directly from engineered microbial cultures, establishing a new class of cell-free biosensors. We found that kinetically-controlled ribosensors exhibited 5-10 fold greater ligand sensitivity than a thermodynamically-controlled device. And, we further demonstrated that a second aptamer, promiscuous for aromatic amino acid binding, could be assembled into kinetic ribosensors with 45-fold improvements in ligand selectivity. These results have broad implications for engineering RNA aptamer devices and overcoming thermodynamic constraints on molecular recognition through the design of kinetically-controlled responses.
Smad9 is a key player of follicular selection in goose via keeping the balance of LHR transcription
Authors: Yu Daolun , Chen Fanghui , Zhang Li , Wang Hejian , Chen Jie , Zhang Zongmeng , Li Jie , Xing Chaofeng , Li Honglin , Li Jun , Cai Yafei
Published: November 2017

The egg production of poultry depends on follicular development and selection. However, the mechanism of selecting the priority of hierarchical follicles is completely unknown. Smad9 is one of the important transcription factors in BMP/Smads pathway and involved in goose follicular initiation. To explore its potential role in goose follicle hierarchy determination, we first blocked Smad9 expression using BMP typeⅠreceptor inhibitor LDN–193189 bothin vivoandin vitro. Unexpectedly, LDN–193189 administration could dramatically suppress Smad9 level and elevate egg production (7.08 eggs / bird,P< 0.05) of animals, and the estradiol (E2) and luteinizing hormone receptor (LHR) level were significantly increased (P< 0.05), but the progesterone (P4) and follicle stimulating hormone receptor (FSHR) mRNA remain unchanged. Surprisingly, Smad9 knockdown notably attenuated (P< 0.05) in E2, P4, FSHR and LHR level in goose granulosa cells (gGCs). Further chromatin immunoprecipitation (ChIP) assay of gGCs revealed that Smad9, served as a sensor of balance, bound to the LHR promoter regulating its transcription. These findings demonstrated that Smad9 is differentially expressed in goose follicles, and acts as a key player in controlling goose follicular selection.

SUMMARY STATEMENT

To study the hierarchical development mechanism of avian follicle, new strategies can be found to improve the egg production of low-yielding poultry, such as geese.
Stochastic dynamics of an epidemics with recurrent spillovers from an endemic reservoir
Authors: Voinson Marina , Alvergne Alexandra , Billiard Sylvain , Smadi Charline
Published: November 2017

Most emerging human infectious diseases have an animal origin. Yet, while zoonotic diseases originate from a primary reservoir, most theoretical studies have principally focused on single-host processes, either exclusively humans or exclusively animals, without considering the importance of animal to human transmission for understanding the dynamics of emerging infectious diseases. Here we aim to investigate the importance of spillover transmission for explaining the number and the size of outbreaks. We propose a simple stochastic Susceptible-Infected-Recovered model with a recurrent infection of an incidental host from a reservoir (e.g. humans by a zoonotic species), considering two modes of transmission, (1) animal-to-human and (2) human-to-human. The model assumes that (i) epidemiological processes are faster than other processes such as demographics or pathogen evolution and (ii) that an epidemic occurs until there are no susceptible individuals left. The results show that during an epidemic, even when the pathogens are barely contagious, multiple outbreaks are observed due to spillover transmission. Overall, the findings demonstrate that the only consideration of direct transmission between individuals is not sufficient to explain the dynamics of zoonotic pathogens in an incidental host.
Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage
Authors: Gonçalves Carla , Wisecaver Jennifer H. , Salema-Oom Madalena , Leandro Maria José , Shen Xing-Xing , Peris David , Hittinger Chris Todd , Rokas Antonis , Gonçalves Paula
Published: November 2017

Fructophily is a rare trait that consists in the preference for fructose over other carbon sources. Here we show that in a yeast lineage (theWickerhamiella/Starmerella, W/S clade) formed by fructophilic species thriving in the floral niche, the acquisition of fructophily is part of a wider process of adaptation of central carbon metabolism to the high sugar environment. Coupling comparative genomics with biochemical and genetic approaches, we show that the alcoholic fermentation pathway was profoundly remodeled in the W/S clade, as genes required for alcoholic fermentation were lost and subsequently re-acquired from bacteria through horizontal gene transfer. We further show that the reinstated fermentative pathway is functional and that an enzyme required for sucrose assimilation is also of bacterial origin, reinforcing the adaptive nature of the genetic novelties identified in the W/S clade. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.
The Hallucination Machine: A Deep-Dream VR platform for Studying the Phenomenology of Visual Hallucinations
Authors: Suzuki Keisuke , Roseboom Warrick , Schwartzman David J. , Seth Anil K.
Published: November 2017

Altered states of consciousness, such as psychotic or pharmacologically-induced hallucinations, provide a unique opportunity to examine the mechanisms underlying conscious perception. However, the phenomenological properties of these states are difficult to isolate experimentally from other, more general physiological and cognitive effects of psychoactive substances or psychopathological conditions. Thus, simulating phenomenological aspects of altered states in the absence of these other more general effects provides an important experimental tool for consciousness science and psychiatry. Here we describe such a tool, theHallucination Machine. It comprises a novel combination of two powerful technologies: deep convolutional neural networks (DCNNs) and panoramic videos of natural scenes, viewed immersively through a head-mounted display (panoramic VR). By doing this, we are able to simulate visual hallucinatory experiences in a biologically plausible and ecologically valid way. Two experiments illustrate potential applications of theHallucination Machine. First, we show that the system induces visual phenomenology qualitatively similar to classical psychedelics. In a second experiment, we find that simulated hallucinations do not evoke the temporal distortion commonly associated with altered states. Overall, theHallucination Machineoffers a valuable new technique for simulating altered phenomenology without directly altering the underlying neurophysiology.
A proposed chaperone of the bacterial type VI secretion system functions to constrain a self-identity protein
Authors: Zepeda-Rivera Martha A. , Saak Christina C. , Gibbs Karine A.
Published: November 2017

The opportunistic bacterial uropathogenProteus mirabiliscan communicate identity through the export of the self-identity protein, IdsD, via the type VI secretion (T6S) system. Expression of theidsgenes provides a fitness advantage during polymicrobial infections in a mouse infection model. Here we provide an answer to the unresolved question of how the activity of a T6S substrate, such as IdsD, is regulated before export. We demonstrate that IdsD is found in clusters that form independently of the T6S machinery and activity. We show that the protein IdsC, which is a member of the proposed DUF4123 chaperone family, is essential for the stability of these clusters as well as the IdsD protein itself. And we provide evidence that amino acid disruptions in IdsC are sufficient to disrupt IdsD export but not IdsD localization into stable subcellular clusters, strongly supporting that IdsC functions in at least two different ways: IdsD stabilization and IdsD export. We propose that IdsC, and likely other DUF4123-containing proteins, function to regulate T6S substrates before export by both stabilizing the protein and mediating export at the T6S machinery.
Learning the pattern of epistasis linking genotype and phenotype in a protein
Authors: Poelwijk Frank J. , Socolich Michael , Ranganathan Rama
Published: November 2017

Understanding the pattern of epistasis – the non-independence of mutations – is critical for relating genotype and phenotype in biological systems. However, the complexity of potential epistatic interactions has limited approaches to this problem at any level. To develop practical strategies, we carried out a comprehensive experimental study of epistasis between all mutations that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein. The data demonstrate significant high-order epistatic interactions between mutations, but also reveals extraordinary sparsity, enabling novel experimental strategies and sequence-based statistical methods for learning the relevant epistasis. The sequence space linking the parental fluorescent proteins is functionally connected through paths of single mutations; thus, high-order epistasis in proteins is consistent with evolution through stepwise variation and selection. This work initiates a path towards characterizing epistasis in proteins in general.
Conductive particles enable syntrophic acetate oxidation between Geobacter and Methanosarcina from coastal sediments
Authors: Rotaru Amelia-Elena , Stryhanyuk Hryhoriy , Calabrese Federica , Musat Florin , Shrestha Pravin Malla , Weber Hannah Sophia , Snoeyenbos-West Oona L.O. , Hall Per O.J. , Richnow Hans H. , Musat Niculina , Thamdrup Bo
Published: November 2017

Coastal sediments are rich in conductive minerals, which could impact microbial processes for which acetate is a central intermediate. In the methanogenic zone, acetate is consumed by methanogens and/or syntrophic acetate oxidizing (SAO) consortia. SAO consortia live under extreme thermodynamic pressure and their survival depends on successful partnership. Here we demonstrate that conductive minerals facilitate a SAO partnership betweenGeobacterandMethanosarcinafrom the coastal sediments of the Bothnian Bay, Baltic Sea. Bothnian methanogenic sediments showed a high apparent isotopic fractionation (αc1.07) characteristic of CO2-reductive methanogenesis. The native community was represented by electrogens such asGeobacterand methanogens likeMethanosarcina. Upon the addition of conductive particles (activated carbon and magnetite) methanogenesis from acetate increased four fold.Geobacter(96% related toG. psychrophilus) andMethanosarcina(99% related toM. subterranea) dominated the conductive particle-spiked SAO communities. Using NanoSIMS we demonstrated that during SAO,Geobacterincorporated 82% of the labeled acetate as compared to only 18% byMethanosarcina. At the same timeGeobacterconverted 27% of the13C-acetate to13CO2as detected by IRMS. Indigenous soluble shuttles were not involved in SAO, since spiking fresh cultures with spent-media filtrate had no effect on methanogenic rates. Our results demonstrate thatGeobacteroxidizes acetate to CO2while transferring electrons extracellularly via conductive particles toMethanosarcina, which utilizes them for CO2reduction to methane. In natural environments, mediation of SAO by conductive particles between electrogens and methanogens could impact the iron and methane cycles.

Significance

Acetate oxidizing bacteria are known to thrive in mutualistic consortia in which H2or formate is shuttled to a methane-producingArchaeapartner. Here we discovered that they could instead transfer electrons via conductive minerals. Mineral-SAO (syntrophic acetate oxidation) could be a vital pathway for CO2-reductive methanogenesis in the environment, especially in sediments rich in conductive minerals. Mineral-SAO is therefore of potential importance for both iron and methane cycles in sediments and soils. Additionally, our observations imply that agricultural runoff or amendments with conductive chars could trigger a significant increase in methane emissions.
An eutherian intronic sequence gave rise to a major satellite DNA in Platyrrhini
Authors: Valeri Mirela Pelizaro , Dias Guilherme Borges , Socorro Pereira Valéria do , Kuhn Gustavo Campos Silva , Svartman Marta
Published: November 2017

Satellite DNAs (satDNAs) are major components of eukaryote genomes. However, because of their quick divergence, the evolutionary origin of a given satDNA family can rarely be determined. Herein we took advantage of available primate sequenced genomes to determine the origin of the CapA satDNA (~1,500 bp long monomers), first described in Sapajus apella. We show that CapA is an abundant satDNA in Platyrrhini, whereas in the genomes of most eutherian mammals, including humans, this sequence is present only as a single copy located within a large intron of the NOS1AP (nitric oxid synthase 1 adaptor protein) Gene. Our data suggest that this intronic CapA-like sequence gave rise to the CapA satDNA and we discuss possible mechanisms implicated in this event. This is the first report of a single copy intronic sequence giving origin to a satDNA that reaches up to 100,000 copies in some genomes.