bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Resistance to Major Tropical Root-Knot Nematodes (Meloidogyne spp.) in Solanum sisymbriifolium
Authors: Hajihassani Abolfazl , Rutter William B. , Schwarz Tanner , Woldemeskel Moges , Ali Md Emran , Hamidi Negin
Published: December 2019

Root-knot nematodes (Meloidogyne spp.) are important contributors to yield reduction in tomato. Though resistant cultivars to common species (Meloidogyne arenaria, M. incognita, and M. javanica) are available, they are not effective against other major species of root-knot nematodes. Cultivars or lines of Solanum sisymbriifolium were examined to assess the presence and level of resistance to five major species: M. arenaria race 1, M. incognita race 3, M. haplanaria, M. javanica, and M. enterolobii. Differences in S. sisymbriifolium response to the nematode infection were apparent when susceptibility or resistance was classified by the egg counts per gram fresh weight of root and the multiplication rate of the nematodes. The cultivar Diamond was highly susceptible, Quattro and White Star were susceptible, while Sis Syn II was resistant to M. arenaria. Quattro, White Star, and Sis Syn II exhibited a moderate to high level of resistance to M. incognita but the nematode increased 2.5-fold from the initial population of the M. incognita on Diamond. All S. sisymbriifolium cultivars were highly resistant to both M. haplanaria and M. enterolobii, while highly susceptible to M. javanica. A microplot study under field conditions using Sis Syn II confirmed that M. arenaria, M. incognita, and M. haplanaria were not pathogenic on the plant. Likewise, an examination on cross-sections of galled root tissues confirmed the susceptibility and resistance of S. sisymbriifolium lines to Meloidogyne spp. Using S. sisymbriifolium as a resistant rootstock or a new source of resistance may result in the development of nonchemical and sustainable management strategies to protect the tomato crop.
CORRELATION BETWEEN POSTERIOR STAPHYLOMA AND DOME-SHAPED MACULA IN HIGH MYOPIC EYES
Authors: Dai Fangfang , Li Shuyin , Wang Yanting , Li Shuangshuang , Han Jinfeng , Li Mengdi , Zhang Zhong , Jin Xuemin , Dou Shewei
Published: December 2019

Purpose:

To investigate the relationship between posterior staphyloma and dome-shaped macula (DSM) in highly myopic eyes.

Methods:

The clinical data were collected from patients with high myopia: diopter, best-corrected visual acuity, axial length, fundus images, optical coherence tomography, and 3D magnetic resonance imaging. A DSM was defined as a convex curvature of the macula in one or both of the vertical and horizontal optical coherence tomography scans. The relationship between DSM and posterior staphyloma was evaluated.

Results:

A total of 123 eyes were included. Dome-shaped macula was found in 18 eyes (14.63%). Twelve eyes with DSM had positive 3D magnetic resonance imaging findings. Nine eyes had horizontal oval-shaped dome, and a band-shaped inward convexity that extended horizontally from the optic disc through the fovea could be seen. Three eyes had round dome, and 3D magnetic resonance imaging showed a round inward convexity of the macular area. Five inward convexities were the border of multiple staphylomas, five were the boundary of one staphyloma, and two were within a single staphyloma.

Conclusion:

The formation of highly myopic DSM is related to the morphological change of the entire posterior segment.
Inflammatory bowel disease versus Chlamydia trachomatis infection: a case report and revision of the literature
Authors: Neri Benedetto , Stingone Christof , Romeo Samanta , Sena Giorgia , Gesuale Cristina , Compagno Mirko , De Cristofaro Elena , Baciorri Francesca , Del Vecchio Blanco Giovanna , Palmieri Giampiero , Sarmati Loredana , Biancone Livia
Published: December 2019

Infectious proctitis may mimic inflammatory bowel disease, particularly when limited to the rectum. The present case report includes findings from a 50-year-old man, soldier, referring to our Inflammatory Bowel Disease Unit with a diagnosis of rectal Crohn’s disease, refractory to conventional treatments. Mild anemia, hypergammaglobulinemia and HIV-antibodies seronegativity were detected. Entero-MRI and stool examinations were negative. Ileocolonoscopy detected few rectal ulcers with irregular edges. Endosonography showed marked thickening of the rectal wall and enlarged perirectal lymphnodes. Nodal and rectal fine needle aspirate did not show atypia (PAN CK-). Rectal biopsies showed flogistic granular tissue (PAN CK-): Warthin-Starry stain was negative. Previous Treponema pallidum infection was detected. Clinical history revealed habits at risk for sexually transmitted infection. Rectal swabs for RT-PCR for Chlamydia trachomatis, Neisseria gonorrhoeae, and Herpes Simplex Virus 1-2 lead to a diagnosis of lymphogranuloma venereum. Doxycycline 100 mg and Azitromicyn 500 mg t.i.d. were given for 21 days, followed by negativity for RT-PCR for Chlamydia trachomatis at rectal swabs. Complete disappearance of symptoms and mucosal healing occurred. Due to the increased frequency of infectious diseases, sexually transmitted infection (including lymphogranuloma venereum) should be considered as possible differential diagnosis when assessing patients with inflammatory bowel disease limited to the rectum.
Transjugular intrahepatic portosystemic shunt for patients with liver cirrhosis: survey evaluating indications, standardization of procedures and anticoagulation in 43 German hospitals
Authors: Steib Christian J. , Li Hanwei , Zhang Jiang , Mayerle Julia , Ricke Jens , Gerbes Alexander L. , Meyer Carsten , Zipprich Alexander , Trebicka Jonel
Published: December 2019

Objectives

Transjugular intrahepatic portosystemic shunt (TIPS) insertion is an established treatment to lower portal pressure. There are no obligatory evidence-based recommendations addressing procedure and anticoagulation. Therefore, a survey was performed to establish current practice at different German hospitals.

Methods

A three-page survey was sent out via postal mail to 76 different hospitals addressing the topics indication, contraindication, follow-up and anticoagulation.

Results

Forty-three hospitals completed the survey: the median number of TIPS/year was 28.6 ± 23. Ascites and hydrothorax were announced as the main indications. Bilirubin levels above 5 mg/dl, hepatic encephalopathy and cardiac disease were considered as absolute contraindications in most hospitals, but age was not. The biggest variations were reported with regard to anticoagulation after TIPS procedure. Four hospitals never used any anticoagulation; most hospitals reported the use of low molecular weight heparins for a period of days up to 4 weeks. But also aspirin or clopidogrel was used after TIPS insertion in eight different hospitals. Additionally, the standards for follow-up after TIPS insertion were different in the hospitals.

Conclusions

There is no consensus how to handle indication, contraindications and anticoagulation after the TIPS procedure. A national and international consensus is warranted to improve the outcome of TIPS patients and reduce secondary complications. In addition to compare results and efficacy in the future standard operation procedures as proposed here need to be put in place.
Fully Covered Self-Expandable Metal Stens eliminate surgical repair requirement in both endoscopic sphincterotomy and precut sphincterotomy-related perforation (with video)
Authors: Parlak Erkan , Koksal Aydin Seref , Eminler Ahmet Tarik , Ercan Metin , Toka Bilal , Karaman Kerem , Uslan Mustafa Ihsan
Published: December 2019

Objective

Endoscopic retrograde cholangiopancreatography (ERCP)-related perforations occur in 0.3–0.6% of patients. The treatment of retroperitoneal paravaterian perforations (type II), which develop during endoscopic sphincterotomy or precut sphincterotomy, remains a matter of debate. We aimed to evaluate the efficacy of fully covered self expandable metal stent (Fc-SEMS) placement in the treatment of type II perforations.

Methods

The study was conducted in a tertiary ERCP reference center of Turkey between December 2013 and June 2016. Patients with type II ERCP-related perforation constituted the study group. Type II perforations were treated by insertion of an Fc-SEMS (10 mm × 60 mm) during the ERCP procedure or intraoperatively by surgery-endoscopy rendezvous technique, if biliary cannulation could not be achieved.

Results

A total of 2689 ERCPs were performed. ERCP-related perforation was observed in 12 procedures (0.4%). Eight patients had Stapfer type II perforations, which developed during endoscopic sphincterotomy in seven patients and precut sphincterotomy in one patient. Fc-SEMSs were inserted during the ERCP procedure in seven patients and intraoperatively by surgery-endoscopy rendezvous technique in one patient. None of the patients developed fever, hemodynamic instability, or peritoneal signs. Stents were removed after a median duration of 9 (3–14) days. All of the patients were uneventfully discharged after an average hospital length of stay of median 5 (1–9) days.

Conclusion

Fc-SEMSs are highly effective in the nonoperative treatment of type II perforations and their intraoperative insertion in patients with unsuccessful cannulation may facilitate surgery by eliminating the need for duodenum repair surgery.
Heme is involved in the systemic inflammatory response following radiofrequency ablation of hepatic hemangiomas
Authors: Yang Xu , Liu Jun , Yang Meng-Meng , Wang Shao-Hong , Xu Li , Ke Shan , Ding Xue-Mei , Sun Wen-Bing , Gao Jun
Published: December 2019

Objective

Radiofrequency ablation (RFA) is an effective and minimally invasive treatment for managing hepatic hemangiomas. Systemic inflammatory response syndrome (SIRS) often occurs with hemoglobinuria, and its underlying pathophysiological mechanism is unknown. Heme can trigger inflammation by inducing the generation of reactive oxygen species (ROS) and the production of inflammatory mediators. We therefore investigated whether circulating heme is involved in SIRS following RFA of hepatic hemangiomas.

Methods

We enrolled 65 patients with hepatic hemangioma who underwent RFA. Serum concentrations of free heme, ROS, and tumor necrosis factor α (TNF-α) were measured after RFA. Univariate analysis and a multivariate binary logistic regression model were used to evaluate the contribution of 17 risk factors for SIRS after RFA.

Results

Fifty-nine (59/65, 90.8%) patients developed hemoglobinuria, among which 25 (25/59, 42.4%) experienced SIRS shortly after RFA. In the SIRS group, the serum concentrations of heme, ROS, and TNF-α were immediately elevated after RFA compared with baseline and slowly regained their normal levels 3 days after RFA. Moreover, the concentrations of circulating heme significantly correlated with those of ROS (r = 0.805, P < 0.001) and TNF-α (r = 0.797, P < 0.001). Multivariate analysis showed that the volume of hemangioma [odds ratio (OR) = 1.293, P = 0.031], time of ablation (OR = 1.194, P = 0.029) as well as the concentrations of heme (OR = 1.430, P = 0.017), ROS (OR = 1.251, P = 0.031), and TNF-α (OR = 1.309, P = 0.032) were significantly associated with SIRS.

Conclusion

Circulating heme was associated with the induction of ROS and the production of TNF-α, which may contribute to the induction of SIRS following RFA of hepatic hemangiomas.
Serial clinical observation for management of newborns at risk of early-onset sepsis
Authors: Berardi Alberto , Bedetti Luca , Spada Caterina , Lucaccioni Laura , Frymoyer Adam
Published: December 2019

Purpose of review

Current management approaches for asymptomatic neonates at risk of early onset sepsis remain controversial. Strategies based entirely on clinical observation (SCO, serial clinical observation) have gained consensus.

Recent findings

We briefly compare different strategies for managing asymptomatic newborns suggested in four high-income countries. Then this review details the existing differences in carrying out the SCO in the United Kingdom, the USA, and Italy; the experiences from the studies performed using the SCO; and open questions regarding this strategy. Advantages and limitations of SCO are also discussed. There is a need to assess which symptoms at birth are more predictive of early onset sepsis and therefore require immediate interventions versus those symptoms that can be monitored and re-evaluated.

SCO strategy may require changes in the processes of newborn care at birthing centers. Nonetheless, SCO is safe and is associated with fewer laboratory evaluations and unnecessary antibiotics. Thoughtful and thorough practices related to the care of all newborns will benefit any birthing centre.

Video abstract

http://links.lww.com/MOP/A40.
Rotavirus vaccination in the neonatal intensive care units: where are we? A rapid review of recent evidence
Authors: Sicard Mélanie , Bryant Kristina , Muller Martha L. , Quach Caroline
Published: December 2019

Purpose of review

Rotavirus is a leading cause of viral acute gastroenteritis in infants. Neonates hospitalized in neonatal intensive care units (NICUs) are at risk of rotavirus infections with severe outcomes. The administration of rotavirus vaccines is only recommended, in the United States and Canada, upon discharge from the NICU despite rotavirus vaccines being proven well tolerated and effective in these populations, because of risks of live-attenuated vaccine administration in immunocompromised patients and theoretical risks of rotavirus vaccine strains shedding and transmission.

We aimed to summarize recent evidence regarding rotavirus vaccine administration in the NICU setting and safety of rotavirus vaccines in preterm infants.

Methods

We conducted a rapid review of the literature from the past 10 years, searching Medline and Embase, including all study types except reviews, reporting on rotavirus vaccines 1 and 5; NICU setting; shedding or transmission; safety in preterm. One reviewer performed data extraction and quality assessment.

Recent findings

Thirty-one articles were analyzed. Vaccine-derived virus shedding following rotavirus vaccines existed for nearly all infants, mostly during the first week after dose 1, but with rare transmission only described in the household setting. No case of transmission in the NICU was reported. Adverse events were mild to moderate, occurring in 10–60% of vaccinated infants. Extreme premature infants or those with underlying gastrointestinal failure requiring surgery presented with more severe adverse events.

Recommendations regarding rotavirus vaccine administration in the NICU should be reassessed in light of the relative safety and absence of transmission of rotavirus vaccine strains in the NICU.
Sudden Death Due to Calcifying Pseudoneoplasm of the Neuraxis
Authors: Conway Kyle S. , Jentzen Jeffrey , Pratt Drew , Camelo-Piragua Sandra
Published: December 2019

We present a case of a 22-year-old man who died unexpectedly after a seizure due to a previously undiagnosed calcifying pseudoneoplasm of the neuraxis (CAPNON). Calcifying pseudoneoplasm of the neuraxis is a rare entity, and this is, to our knowledge, the first described case of sudden death due to CAPNON. Sudden death due to undiagnosed central nervous system mass lesions is rare, and most cases are attributable to hemorrhage, hydrocephalus, or increased intracranial pressure due to mass effect. Seizure is a rare cause of sudden death due to central nervous system mass lesions. This case highlights that mass lesions may cause sudden death due to seizure, even without other pathologic evidence of a cause of death, such as hemorrhage or edema. Furthermore, benign, reactive, and low-grade mass lesions may cause sudden death due to seizure. Seizure should remain in the autopsy differential as a cause of death, even where there is no pathologically evident mechanism by which a mass lesion caused death.
Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects
Authors: Zhang Linyi , Hood Glen R. , Ott James R. , Egan Scott P.
Published: December 2019

Phenological differences between host plants can promote temporal isolation among host-associated populations of insects with life cycles tightly coupled to plant phenology. Divergence in the timing of spring budbreak between two sympatric sister oak species has been shown to promote temporal isolation between host plants and their host-associated populations of a cynipid gall wasp. Here, we examined the generality of this mechanism by testing the hypothesis of cascading temporal isolation for five additional gall-formers and three natural enemy species associated with these same oak species. The timing of adult emergence from galls differed significantly between host-associated populations for all nine species and parallels the direction of the phenological differences between host plants. Differences in emergence timing can reduce gene flow between host-associated populations by diminishing mating opportunities and/or reducing the fitness of immigrants due to differences in the availability of ephemeral resources. Our study suggests that cascading temporal isolation could be a powerful ‘biodiversity generator’ across multiple trophic levels in tightly coupled plant–insect systems.
Phylogenetic aggregation increases zoonotic potential of mammalian viruses
Authors: Park Andrew W.
Published: December 2019

While many viruses of wild mammals are capable of infecting humans, our understanding of zoonotic potential is incomplete. Viruses vary in their degree of generalism, characterized by the phylogenetic relationships of their hosts. Among the dimensions of this phylogenetic landscape, phylogenetic aggregation, which is largely overlooked in studies of parasite host range, emerges in this study as a key predictor of zoonotic status of viruses. Plausibly, viruses that exhibit aggregation, typified by discrete clusters of related host species, may (i) have been able to close the phylogenetic distance to humans, (ii) have subsequently acquired an epidemiologically relevant host and (iii) exhibit relatively high fitness in realized host communities, which are frequently phylogenetically aggregated. These mechanisms associated with phylogenetic aggregation may help explain why correlated fundamental traits, such as the ability of viruses to replicate in the cytoplasm, are associated with zoonoses.
Electromagnetic 0.1–100 kHz noise does not disrupt orientation in a night-migrating songbird implying a spin coherence lifetime of less than 10 µs
Authors: Kobylkov Dmitry , Wynn Joe , Winklhofer Michael , Chetverikova Raisa , Xu Jingjing , Hiscock Hamish , Hore P. J. , Mouritsen Henrik
Published: December 2019

According to the currently prevailing theory, the magnetic compass sense in night-migrating birds relies on a light-dependent radical-pair-based mechanism. It has been shown that radio waves at megahertz frequencies disrupt magnetic orientation in migratory birds, providing evidence for a quantum-mechanical origin of the magnetic compass. Still, many crucial properties, e.g. the lifetime of the proposed magnetically sensitive radical pair, remain unknown. The current study aims to estimate the spin coherence time of the radical pair, based on the behavioural responses of migratory birds to broadband electromagnetic fields covering the frequency band 0.1–100 kHz. A finding that the birds were unable to use their magnetic compass under these conditions would imply surprisingly long-lived (greater than 10 µs) spin coherence. However, we observed no effect of 0.1–100 kHz radiofrequency (RF) fields on the orientation of night-migratory Eurasian blackcaps (Sylvia atricapilla). This suggests that the lifetime of the spin coherence involved in magnetoreception is shorter than the period of the highest frequency RF fields used in this experiment (i.e. approx. 10 µs). This result, in combination with an earlier study showing that 20–450 kHz electromagnetic fields disrupt magnetic compass orientation, suggests that the spin coherence lifetime of the magnetically sensitive radical pair is in the range 2–10 µs.
Asmodochelys parhami, a new fossil marine turtle from the Campanian Demopolis Chalk and the stratigraphic congruence of competing marine turtle phylogenies
Authors: Gentry Andrew D. , Ebersole Jun A. , Kiernan Caitlin R.
Published: December 2019

Resolving the phylogeny of sea turtles is uniquely challenging given the high potential for the unification of convergent lineages due to systematic homoplasy. Equivocal reconstructions of marine turtle evolution subsequently inhibit efforts to establish fossil calibrations for molecular divergence estimates and prevent the accurate reconciliation of biogeographic or palaeoclimatic data with phylogenetic hypotheses. Here we describe a new genus and species of marine turtle,Asmodochelys parhami, from the Upper Campanian Demopolis Chalk of Alabama and Mississippi, USA represented by three partial shells. Phylogenetic analysis shows thatA. parhamibelongs to the ctenochelyids, an extinct group that shares characteristics with both pan-chelonioids and pan-cheloniids. In addition to supporting Ctenochelyidae as a sister taxon of Chelonioidea, our analysis places Protostegidae outside of the Chelonioidea crown group and recoversAllopleuron hofmannias a stem dermochelyid. Gap excess ratio (GER) results indicate a strong stratigraphic congruence of our phylogenetic hypothesis; however, the highest GER value is associated with the phylogenetic hypothesis of marine turtles which excludes Protostegidae from the Cryptodira crown group. Ancestral range estimations derived from our phylogeny imply a European or North American origin of Chelonioidea in the middle-to-late Campanian, approximately 20 Myr earlier than current molecular divergence studies suggest.
Agromyces protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis
Authors: Heo Jun , Hamada Moriyuki , Tamura Tomohiko , Saito Satomi , Lee Soon Dong , Kim Jeong-Seon , Hong Seung-Beom , Kwon Soon-Wo , Kim Soo-Jin
Published: December 2019

An actinobacterial strain, designated FW100M-8T, was isolated from a gut sample of larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, South Korea. Cells were Gram-stain-positive, microaerophilic to aerobic, non-spore forming and non-motile. It grew at pH 7.0–9.0 (optimum, pH 8.0), at 15–35 °C (optimum, 28 °C) and 0–3.0 % (w/v) NaCl (optimum, 0 %). According to the 16S rRNA gene analysis, strain FW100M-8T shared the highest sequence similarity with

Agromyces mediolanus

DSM 20152T (98.4 %),

Agromyces ulmi

XIL01T (98.3 %),

Agromyces indicus

NIO-1018T (98.3 %),

Agromyces soli

MJ21T (98.3 %), and Agromyces arachidis AK-1T (97.9 %). Phylogenetic trees showed that strain FW100M-8T fell into the lineage of the genus

Agromyces

. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The menaquinones of strain FW100M-8T were MK-12 (46 %), MK-11 (36 %), MK-10 (14 %) and MK-13 (4 %). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The peptidoglycan type was supposed to be the type B1, comprising d-Ala, d-Glu, Gly and l-A2bu. The G+C content of the genomic DNA is 70.5 mol%. On the basis of the genotypic and phenotypic data, we conclude that strain FW100M-8T represents a novel species of the genus

Agromyces

, for which the name Agromyces protaetiae sp. nov. is proposed with strain FW100M-8T (=KACC 19308T=NBRC 113048T) as the type strain.
Lacibacter luteus sp. nov., isolated from a freshwater river
Authors: Sheu Shih-Yi , Chen Tzu-Ying , Kwon Soon-Wo , Chen Wen-Ming
Published: December 2019

An isolate, designated TTM-7T, recovered from a freshwater river in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-7Tis affiliated with species in the genusLacibacter. Strain TTM-7Twas most closely related toLacibacter cauensisNJ-8Twith a 98.2 % 16S rRNA gene sequence similarity, followed byLacibacter daechungensisH32-4T(97.4 %) andLacibacter nakdongensisSS2-56T(96.3 %). Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed orange colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. The major fatty acids of strain TTM-7Twere iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6cand/or iso-C15 : 02-OH) and iso-C15 : 1G. The predominant hydroxy fatty acid was iso-C17 : 03-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminoglycolipids, five unidentified aminophospholipids and one unidentified lipid. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TTM-7Twas 40.6 mol%. Strain TTM-7Tshowed 83.6 % average nucleotide identity and 16.0 % digital DNA–DNA hybridization identity withLacibacter cauensisNJ-8T. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TTM-7Tshould be classified in a novel species of the genusLacibacter, for which the nameLacibacter luteussp. nov. is proposed. The type strain is TTM-7T(=BCRC 81159T=LMG 30926T=KCTC 62870T).
Pararobbsia silviterrae gen. nov., sp. nov., isolated from forest soil and reclassification of Burkholderia alpina as Pararobbsia alpina comb. nov.
Authors: Lin Qin-hua , Lv Ying-ying , Gao Zeng-hong , Qiu Li-hong
Published: December 2019

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, DHC34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China (112° 31′ E 23° 10′ N). It grew optimally on R2A medium at 28 °C, at pH 6.0–7.0 and in the presence of 0–1 % (w/v) NaCl. Strain DHC34T was closely related to

Burkholderia alpina

LMG 28138T (98.5 % 16S rRNA gene sequence similarity). 16S rRNA gene sequence analysis showed that strain DHC34T formed a clade with

B. alpina

LMG 28138T, which is next to but branched deeply with

Robbsia andropogonis

ICMP 2807T. The phylogenetic relationships among these three strains were also supported with the phylogram based on concatenated partial gyrB, recA and trpB gene sequences. The phylogenomic tree generated with the UBCG tool showed that strains DHC34T and

R. andropogonis

ICMP 2807T were in a different clade. The DNA–DNA relatedness values between strain DHC34T and

B. alpina

LMG 28138T and

R. andropogonis

ICMP 2807T were much lower than 70 %. Strain DHC34T contained ubiquinone 8 as the major respiratory quinone. Its major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The DNA G+C content of strain DHC34T was 64.2 mol%. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, three unidentified aminophospholipids, four unidentified phospholipids, one unidentified aminolipid and a polar lipid. The phenotypic, phylogenetic, genotypic and chemotaxonomic data showed that strain DHC34T represents a novel species of a new genus in the family

Burkholderiaceae

, for which the name Pararobbsia silviterrae gen. nov., sp. nov. is proposed. The type strain of Pararobbsia silviterrae is DHC34T (=KCTC 42628T=LMG 28845T). On the basis of the current data,

Burkholderia alpina

is renamed as Pararobbsia alpina comb. nov.
Amycolatopsis acidicola sp. nov., isolated from peat swamp forest soil
Authors: Teo Wee Fei Aaron , Srisuk Nantana , Duangmal Kannika
Published: December 2019

A novel actinobacterial strain, designated K81G1T, was isolated from a soil sample collected in Kantulee peat swamp forest, Surat Thani Province, Thailand, and its taxonomic position was determined using a polyphasic approach. Optimal growth of strain K81G1Toccurred at 28–30 °C, at pH 5.0–6.0 and without NaCl. Strain K81G1Thad cell-wall chemotype IV (meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and galactose as diagnostic sugars) and phospholipid pattern type II, characteristic of the genusAmycolatopsis. It contained MK-9(H4) as the predominant menaquinone, iso-C16 : 0, C17 : 0cyclo and C16 : 0as the major cellular fatty acids, and phospholipids consisting of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. Based on 16S rRNA gene sequence similarity and phylogenetic analyses, strain K81G1Twas most closely related toAmycolatopsis rhizosphaeraeTBRC 6029T(97.8 % similarity),Amycolatopsis acidiphilaJCM 30562T(97.8 %) andAmycolatopsis bartoniaeDSM 45807T(97.6 %). Strain K81G1Texhibited low average nucleotide identity and digital DNA–DNA hybridization values withA. rhizosphaeraeTBRC 6029T(76.4 %, 23.0 %),A. acidiphilaJCM 30562T(77.9 %, 24.6 %) andA. bartoniaeDSM 45807T(77.8 %, 24.3 %). The DNA G+C content of strain K81G1Twas 69.7 mol%. Based on data from this polyphasic study, strain K81G1Trepresents a novel species of the genusAmycolatopsis, for which the nameAmycolatopsis acidicolasp. nov. is proposed. The type strain is K81G1T(=TBRC 10047T=NBRC 113896T).
Strategy in wheat-Fusariumdual-genome RNA-seq data processing
Authors: Liu Ziying , Li Yifeng , Pan Youlian , Wang Lipu , Ouellet Therese , Fobert Pierre
Published: December 2019

In RNA-seq data processing, short read alignments are usually of one species against its own genome; however, in plant-microbe interaction systems, reads from both host and pathogen samples are blended together. In contrast to single-genome, both pathogen and host reference genomes are involved in the alignment process. In such circumstances, the order of alignment to the host, the pathogen, or simultaneously to both genomes results in differences in read counts of certain genes, especially at the advanced infection stage. It is crucial to have an appropriate strategy for aligning the reads to their respective genomes, yet the existing strategies of either sequential or parallel alignment become a problem when mapping mixed reads to their corresponding reference genomes. The challenge lies in the determination of which reads belong to which species, especially when homology exists between the two genomes.

This study proposes a combo-genome alignment strategy after comparing three alignment scenarios. Simulation results demonstrated that the degree of discrepancy in the results is correlated with phylogenetic distance of the two species in the mixture which was attributable to the extent of homology between the two genomes involved. This correlation was also found in the analysis using two real RNA-seq datasets ofFusarium-challenged wheat plants. Comparisons of the three RNA-seq processing strategies on three simulation datasets and two realFusarium-infected wheat datasets showed that an alignment to a combo-genome, consisting of both host and pathogen genomes, improves mapping quality as compared to sequential alignment procedures.
Sequence Comparison without Alignment: TheSpaMapproaches
Authors: Morgenstern Burkhard
Published: December 2019

Sequence alignment is at the heart of DNA and protein sequence analysis. For the data volumes that are nowadays produced by massively parallel sequencing technologies, however, pairwise and multiple alignment methods have become too slow for many data-analysis tasks. Therefore, fast alignment-free approaches to sequence comparison have become popular in recent years. Most of these approaches are based onword frequencies, for words of a fixed length, or on word-matchingstatistics. Other approaches are based on the length ofmaximal word matches. While these methods are very fast, most of them are based on ad-hoc measures of sequences similarity or dissimilarity that are often hard to interpret. In this review article, I describe a number of alignment-free methods that we developed in recent years. Our approaches are based onspaced word matches (‘SpaM’), i.e. on inexact word matches, that are allowed to contain mismatches at certain pre-defined positions. Unlike most previous alignment-free approaches, our approaches are able to accurately estimate phylogenetic distances between DNA or protein sequences based on stochastic models of molecular evolution.
F1000ResearchTMATCH: A New Algorithm for Protein Alignments using amino-acid hydrophobicities
Authors: Cavanaugh David , Chittur Krishnan
Published: December 2019

The identification of proteins of similar structure using sequence alignment is an important problem in bioinformatics. We decribe TMATCH, a basic dynamic programming alignment algorithm which can rapidly identify proteins of similar structure from a database. TMATCH was developed to utilize an optimal hydrophobicity metric for alignments traceable to fundamental properties of amino-acids. Standard alignment algorithms use affine gap penalties as contrasted with the TMATCH algorithm adaptation of local alignment score reinforcement of favorable diagonal paths (transitions) and punishment of unfavorable transitions paired with fixed gap opening penalties. The TMATCH algorithm is especially designed to take advantage of the extra information available within the hydrophobicity scale to detect homologies, as opposed to the probabilities derived from raw percent identities.
Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes
Authors: Garge Riddhiman K. , Laurent Jon M. , Kachroo Aashiq H. , Marcotte Edward M.
Published: December 2019

Many gene families have been expanded by gene duplications along the human lineage, relative to ancestral opisthokonts, but the extent to which the duplicated genes function similarly is understudied. Here, we focused on structural cytoskeletal genes involved in critical cellular processes including chromosome segregation, macromolecular transport, and cell shape maintenance. To determine functional redundancy and divergence of duplicated human genes, we systematically humanized the yeast actin, myosin, tubulin, and septin genes, testing ∼85% of human cytoskeletal genes across 7 gene families for their ability to complement a growth defect induced by deletion of the corresponding yeast ortholog. In 5 of 7 families—all but α-tubulin and light myosin, we found at least one human gene capable of complementing loss of the yeast gene. Despite rescuing growth defects, we observed differential abilities of human genes to rescue cell morphology, meiosis, and mating defects. By comparing phenotypes of humanized strains with deletion phenotypes of their interaction partners, we identify instances of human genes in the actin and septin families capable of carrying out essential functions, but apparently failing to interact with components of the yeast cytoskeleton, thus leading to abnormal cell morphologies. Overall, we show that duplicated human cytoskeletal genes appear to have diverged such that only a few human genes within each family are capable of replacing the essential roles of their yeast orthologs. The resulting yeast strains with humanized cytoskeletal components now provide surrogate platforms to characterize human genes in simplified eukaryotic contexts.
Reconstructing the complex evolutionary history of the fused Aco2 gene in fission yeast
Authors: Sun Steven , Roy Scott William , Anderson Noelle
Published: December 2019

The Aco2 gene ofSchizosaccharomyces pombewas formed by gene fusion between curious partners, namely genes encoding the enzyme aconitase and a mitochondrial ribosomal protein. In addition to a full-length transcript, a truncated mRNA encoding only the N-terminal aconitase domain is produced by polyadenylation at an internal site. Protein products of the gene are found in the nucleus, mitochondria and cytoplasm, consistent with the presence of multiple subcellular targeting signals. To reconstruct the evolution of this complex gene, we studied homologous genes from a range of related species. We find evidence for a dynamic history within Taphrinomycotina, including: early evolution of a nuclear localization signal; creation of a 3’ intron that could be involved in regulating subcellular targeting; evolution of multiple peroxisomal targeting signals in different lineages; and recurrent gene loss. We present a likely stepwise model for the evolution of this remarkable gene and discuss alternative scenarios.
Separable functions of Tof1/Timeless in intra-S-checkpoint signalling, replisome stability and DNA topological stress
Authors: Westhorpe Rose , Keszthelyi Andrea , Minchell Nicola E. , Jones David , Baxter Jonathan
Published: December 2019

The highly conserved Tof1/Timeless proteins minimise replication stress and promote normal DNA replication. They are required to mediate the DNA replication checkpoint (DRC), the stable pausing of forks at protein fork blocks, the coupling of DNA helicase and polymerase functions during replication stress (RS) and the preferential resolution of DNA topological stress ahead of the fork. Here we demonstrate that the roles of theSaccharomyces cerevisiaeTimeless protein Tof1 in DRC signalling and resolution of DNA topological stress require distinct N and C terminal regions of the protein, whereas the other functions of Tof1 are closely linked to the stable interaction between Tof1 and its constitutive binding partner Csm3/Tipin. By separating the role of Tof1 in DRC from fork stabilisation and coupling, we show that Tof1 has distinct activities in checkpoint activation and replisome stability to ensure the viable completion of DNA replication following replication stress.
ABHD4-dependent developmental anoikis protects the prenatal brain from pathological insults
Authors: László Zsófia I. , Lele Zsolt , Zöldi Miklós , Miczán Vivien , Mógor Fruzsina , Simon Gabriel M. , Mackie Ken , Kacskovics Imre , Cravatt Benjamin F. , Katona István
Published: December 2019

In light of the astronomical number of cell divisions taking place in restricted neurogenic niches, brain malformations caused by ectopic proliferation of misplaced progenitor cells are surprisingly rare. Here, we show that a process we term developmental anoikis distinguishes the abnormal detachment of progenitor cells from the normal delamination of daughter neuroblasts in the developing mouse neocortex. By usingin vivogain-of-function, loss-of-function, and rescue manipulations together with correlated confocal and super-resolution imaging, we identify the endocannabinoid-metabolizing enzyme abhydrolase domain containing 4 (ABHD4) as an essential mediator for the elimination of abnormally detached cells. Consequently, rapid ABHD4 downregulation is necessary for delaminated daughter neuroblasts to escape from anoikis. Moreover, ABHD4 is required for fetal alcohol-induced apoptosis, but not for the well-established form of developmentally controlled programmed cell death. These results suggest that ABHD4-mediated developmental anoikis specifically protects the embryonic brain from the consequences of sporadic delamination errors and teratogenic insults.
Mechanics of multi-centrosomal clustering in bipolar mitotic spindles
Authors: Chatterjee S , Sarkar A , Zhu J , Khodjakov A , Mogilner A , Paul R
Published: December 2019

To segregate chromosomes in mitosis, cells assemble mitotic spindle, a molecular machine with centrosomes at two opposing cell poles and chromosomes at the equator. Microtubules and molecular motors connect the poles to kinetochores, specialized protein assemblies on the centromere regions of the chromosomes. Bipolarity of the spindle is crucial for the proper cell division, and two centrosomes in animal cells naturally become two spindle poles. Cancer cells are often multi-centrosomal, yet they are able to assemble bipolar spindles by clustering centrosomes into two spindle poles. Mechanisms of this clustering are debated. In this study, we computationally screen effective forces between a) centrosomes, b) centrosomes and kineto-chores, c) centrosomes and chromosome arms, d) centrosomes and cell cortex, to understand mechanics that determines three-dimensional spindle architecture. To do this, we use stochastic Monte Carlo search for stable mechanical equilibria in effective energy landscape of the spindle. We find that the following conditions have to be met to robustly assemble the bipolar spindle in a multi-centrosomal cell: 1) strengths of centrosomes’ attraction to each other and to the cell cortex have to be proportional to each other; 2) strengths of centrosomes’ attraction to kinetochores and repulsion from the chromosome arms have to be proportional to each other. We also find that three other spindle configurations emerge if these conditions are not met: a) collapsed, b) monopolar, c) multipolar spindles, and the computational screen reveal mechanical conditions for these abnormal spindles.

Significance statement

To segregate chromosomes, cells assemble bipolar mitotic spindle. Multiple mechanical forces generated by microtubules and molecular motors in the spindle govern the spindle architecture, but it is unclear what force balances support the bipolarity of the spindle. This problem is especially difficult and important in cancer cells, which often have multiple centrosomes that somehow are able to cluster into two spindle poles. By using stochastic energy minimization in an effective energy landscape of the spindle and computationally screening forces, we find mechanical conditions for mono-, multi- and bi-polar spindles. We predict how microtubule and motor parameters have to be regulated in mitosis in multi-centrosomal cells.
Tuning the optical isotropic point of mixed crystals of ethylenediammonium sulfate/selenate
Authors: Tan Melissa , Martin Alexander T. , Shtukenberg Alexander G. , Kahr Bart
Published: December 2019

In anisotropic crystals, optical isotropic points are wavelengths where linear birefringence disappears because the refractive indices for both eigenmodes are accidentally equivalent. Here, the optical isotropic point of ethylenediammonium selenate (EDSe) is tuned by generating a solid-solution series of EDSe doped with sulfate. Mueller matrix polarimetry and single-crystal X-ray diffraction are used to correlate changes in linear birefringence with the crystal composition of EDS
x
Se1−x
. A scheme for using mixed crystals with isotropic points as tunable birefringent optical bandpass filters is proposed and their performance is modeled.
The nondestructive measurement of strain distributions in air plasma sprayed thermal barrier coatings as a function of depth from entire Debye–Scherrer rings
Authors: Li Chun , Xiao Ping , Cernik Robert
Published: December 2019

The residual strain distribution has been measured as a function of depth in both top coat and bond coat in as-received and heat-treated air plasma sprayed thermal barrier coating samples. High-energy synchrotron X-ray beams were used in transmission to produce full Debye–Scherrer rings whose non-circular aspect ratio gave the in-plane and out-of-plane strains far more efficiently than the sin2ψ method. The residual strain in the bond coat is found to be tensile and the strain in the β phase of the as-received sample was measured. The residual strains observed in the top coat were generally compressive (increasing towards the interface), with two kinds of nonlinear trend. These was a `jump' feature near the interface, and in some cases there was another `jump' feature near the surface. It is shown how these trend differences can be correlated to cracks in the coating.
On the puzzling case of sodium saccharinate 1.875-hydrate: structure description in (3+1)-dimensional superspace
Authors: Rekis Toms , Schönleber Andreas , van Smaalen Sander
Published: December 2019

The structure of sodium saccharinate 1.875-hydrate is presented in three- and (3+1)-dimensional space. The present model is more accurate than previously published superstructures, due to an excellent data set collected up to a high resolution of 0.89 Å−1. The present study confirms the unusual complexity of the structure comprising a very large primitive unit cell with Z′ = 16. A much smaller degree of correlated disorder of parts of the unit cell is found than is present in the previously published models. As a result of pseudo-symmetry, the structure can be described in a higher-dimensional space. The X-ray diffraction data clearly indicate a (3+1)-dimensional periodic structure with stronger main reflections and weaker superstructure reflections. Furthermore, the structure is established as being commensurate. The structure description in superspace results in a four times smaller unit cell with an additional base centring of the lattice, resulting in an eightfold substructure (Z′ = 2) of the 3D superstructure. Therefore, such a superspace approach is desirable to work out this high-Z′ structure. The displacement and occupational modulation of the saccharinate anions have been studied, as well as their conformational variation along the fourth dimension.
Combating police corruption in Japan: new challenges ahead?
Authors: Oyamada Eiji
Published: December 2019

Purpose

The purpose of this paper is to analyze Japanese police corruption and assess the effectiveness of the police reforms to minimize it.

Design/methodology/approach

This paper focusses on police corruption in Japan by analyzing its causes and evaluating the effectiveness of measures to prevent it. The paper concludes with some recommendations for minimizing police corruption in Japan.

Findings

Even though recent preventive measures in Japan initiated through police reforms have reduced opportunities for police corruption, it is still necessary to improve public trust in the police. The Japanese police do not initiate anti-corruption measures, but focus instead on prevention through ethics training and reliance on stringent regulations. Fostering a civil society coalition for monitoring police corruption, conducting public perceptions surveys of corruption and bringing police corruption studies into academic discussions are tools for tackling police corruption.

Originality/value

This paper will be useful for scholars, policy-makers and anti-corruption practitioners interested in learning how the Japanese police prevent corruption.
Trust and the intent to cooperate in energy performance contracting for public buildings in China
Authors: Jiang Weiping , Zhao Xianbo
Published: December 2019

Purpose

The purpose of this paper is to explore the key factors in generating trust, and the effects of trust on the intention to cooperate in energy performance contracting (EPC), from the perspective of energy saving companies (ESCOs).

Design/methodology/approach

A questionnaire survey was undertaken to collect the data from the experienced project managers in ESCOs. Structural equation modeling was used to test the hypotheses.

Findings

The results revealed that competence, integrity, communication, reciprocity and contract had positive effects on calculative trust and relational trust. Both calculative trust and relational trust, in turn, were found to have positive effects on the intention to cooperate.

Research limitations/implications

The conclusions are derived from the Chinese cultural background and may apply to a certain geographical scope. In addition, this study focused on the perspective of ESCOs but did not consider that of facility owners.

Practical implications

This research would supply guidance for facility owners or users to cultivate trust from ESCOs and achieve cooperation in EPC.

Originality/value

Most of the existing studies have focused on the perspective of facility owners while few have attempted to investigate the perspective of ESCOs. This study contributes to the knowledge body relating to EPC by investigating the relationship between trust and the intention to cooperate from the perspective of ESCOs. In addition, most EPC studies recognized trust as a condition for the successful execution of EPC projects but failed to consider the role of trust in setting up the cooperation relationship prior to project execution.