bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporating egg-transporting pathways into conservation plans of spawning areas: An example of small yellow croaker (Larimichthys polyactis) in the East China Sea zone
Authors: Liu Zunlei , Jin Yan , Yang Linlin , Yan Liping , Zhang Yi , Xu Min , Tang Jianhua , Zhou Yongdong , Hu Fen , Cheng Jiahua
Published: October 2022

Backward-in-time Lagrangian model can identify potential spawning areas by reconstructing egg drift trajectories, contributing to accurately designing potential priority conservation plans for spawning areas. In this study, we apply this approach to investigate the small yellow croaker (Larimichthys polyactis) with commercial value in China. A two-step spatial random forest (RF) model is used to predict the occurrence probability and abundance of their eggs and describe the optimal ecological range of environmental factors. A priority protection index (BPPI) of the spawning areas is established by combining the sites with the optimal occurrence and abundance and integrating backward tracking pathways. The result indicates that the model with 1-2 day time lags of environmental variables shows the optimum explanatory power. Temperature and salinity are the most important factors affecting oogenesis and show a regime shift in the response curve. They reflect the physiological regulation of parental sexual maturation by the environment. In addition, egg abundance correlates more strongly with chlorophyll-a (Chl a) concentration and depth, suggesting that parents prefer environments with shallow water and high prey density for spawning activities. The egg retrieval shows that the potential spawning sources are distributed near the southeastern part of the oogenesis site, with a maximum egg dispersal distance of no more than 30 km. This finding confirms that the coastal regions of Jiangsu Province are an important spawning ground for the small yellow croaker, making a significant contribution to the productivity and resilience of the fish.
Delineation of estuarine ecological corridors using the MaxEnt model to protect marine fishery biodiversity
Authors: He Yanlong , Zhao Lixia , Liu Shouhai , Zhao Xin , Wang Yutan , Jiang Xiaoshan
Published: October 2022

Ecological corridors (ECs) are important management tools to protect biodiversity by linking fragile habitats, especially for highly mobile organisms. ECs in terrestrial landscapes work as passages on land or in water. However, the significance of ECs to migratory species in estuaries has not been well elucidated. Based on annual fishery investigation in the Yangtze estuary and their dominance index rank, three of the top five species, including Larimochthys polyactis, Coilia mystus, and Gobiidae, exhibited absolute dominance in spring during the past 5 years. The temporal and spatial density variance of C. mystus supported its short-distance migration pattern. Redundancy analysis and the MaxEnt model predicted optimum habitats for C. mystus. C. mystus larvae survival was significantly related to salinity, total nitrogen, pH, reactive silicate, dissolved oxygen, surface water temperature, and chlorophyll-a in May and to salinity, surface water temperature, permanganate index, suspended particles, total nitrogen, and total phosphorus in August. The MaxEnt model predicted a broader longitudinal distribution range from offshore to the upstream freshwater area but narrower latitudinal distribution in the southern branch in May than in August. Finally, we delineated migratory corridors connecting optimum habitats for C. mystus using the least-cost route method. Optimum habitats close to the coastlines in the south branch might play a significant role in maintaining population or community connectivity in the Yangtze estuary. Our findings provide a perspective and method to quantify and facilitate the harmonious development of socioeconomy and fishery biodiversity conservation.
Comparative biology of the grenadiers Macrourus caml and M. whitsoni in the Ross Sea region, Antarctica
Authors: Moore Bradley R. , Parker Steven J. , Marriott Peter M. , Sutton Colin , Pinkerton Matthew H.
Published: October 2022

The grenadiersMacrourus camlandM. whitsoniform a significant bycatch component of longline fisheries for Antarctic toothfish (Dissostichus mawsoni) in the Southern Ocean. A lack of species-level biological and catch data has to date hindered the development of quantitative assessments for these deepwater species. This paper examines species- and sex-specific life histories ofM.camlandM.whitsoniin the Ross Sea region, Antarctica, from samples collected from the commercial fishery and research collections.Macrourus camlwas found to live longer, grow slower, and attain a larger maximum length thanM.whitsoni, reaching at least 65 years of age and 97 cm total length (TL) vs. 43 years and 78 cm TL forM.whitsoni. In addition,M.camlattains a larger length for a given age and a greater weight for a given length. For each species, females of a given age were larger and reached a greater maximum age than males. Assuming that selectivity of the fishing gear is related to fish size, greater fishing pressure on females than males is likely, and was evidenced by female-biased sex ratios of both species. Estimates of natural and fishing mortality rates were low for both species. Despite having a shorter lifespan and attaining a smaller maximum length,M.whitsonimatured later in life and at larger lengths thanM.caml. Although sampling opportunities are constrained seasonally due to sea ice cover, gonad staging and interannual patterns in gonadosomatic indices suggest prolonged spawning for both species, with available data indicating peak spawning during austral summer. The differences in life history observed between these two closely related and morphologically similar species illustrates the importance of understanding species-specific life histories to infer responses to exploitation, provide key biological inputs to inform parameters for future risk assessments and ecosystem models as well as baseline information for comparative work over both time and space, contribute to greater clarity in managing fisheries that interact with these two species, and further our understanding of grenadier life history.
Bamboo fiber reinforced polypropylene composites for transportation applications
Authors: Wasti Sanjita , Kore Surbhi , Yeole Pritesh , Tekinalp Halil , Ozcan Soydan , Vaidya Uday
Published: October 2022

The Apitong wood species has long been the most popular choice for transportation, such as in trailer decking and shipping container floors. However, Apitong is depleting due to its excessive usage. Bamboo fiber provides as an alternative due to its low density (608–780 kg/m3) and lightweight attributes. This study explores 1) development and properties of bamboo-thermoplastic composites with different fiber content, and 2) application of bamboo composite in trailer decking (a transportation application) as an alternative to Apitong. Extrusion-compression and compression molding was used as processing approaches for the bamboo-thermoplastic composites. The basic panels were tested for flexural loading and nail pull out to evaluate the feasibility as a viable trailer decking material. The flexural strength and modulus of bamboo composite were found to be 17 and 98% higher than Apitong, respectively. The density of the bamboo-thermoplastic was 670 kg/m3 compared to Apitong (737 kg/m3), hence 10% lighter. The nail pull-out strength was comparable between the two. The work progressed to producing prototype trailer decking members via extrusion-compression and compression molding. The bamboo-composite decking was evaluated on a trailer test bed and exhibited excellent surface wear response, minimal internal damage and withstood 400 fatigue cycles with onset of failure only at the supports, which the span did not exhibit damage.
Investigating cylinder deactivation as a low fuel-penalty thermal management strategy for heavy-duty diesel engines
Authors: Hushion Christian , Thiruvengadam Arvind , Pondicherry Rasik , Thompson Gregory , Baltrucki Justin , Janak Robb , Lee Justin , Farrell Lisa
Published: October 2022

The upcoming ultra-low-NOx (oxides of nitrogen) emissions standard and in-use NOx emissions requirement requires engine manufacturers to further reduce tailpipe NOx emissions by over 90% from the current United States Environmental Protection Agency 2010 heavy-duty emissions standard. To meet ultra-low NOx standards, significant improvements to the NOx reduction capability of the Selective Catalytic Reduction (SCR) system is required. Low-temperature exhaust conditions and the associated fuel penalty in increasing the exhaust temperatures for improving catalyst activity is an engineering challenge to balance lowering NOx emissions while lowering fuel consumption. Cylinder Deactivation (CDA) in diesel engines has shown the ability to increase exhaust temperatures while maintaining a zero-fuel penalty. This study details the results of the performance of a CDA hardware installed in a modern heavy-duty diesel engine. The study was aimed at developing steady-state engine calibrations to maximize exhaust temperatures while realizing a zero-fuel penalty or improved BTE operation during low-load engine operating conditions for an on-road heavy-duty diesel engine. In addition, the study demonstrated the effect of CDA on lowering aftertreatment cooldown during motoring operation. The results of the study showed close to a 100°C increase in turbine out temperatures (TOT) at idle, 1,000 rpm and 1,200 rpm engine speeds with engine load at 10 and 20% of rated torque. The results also showed that deactivating three of the six cylinders during motoring operation of the low-load cycle delayed after treatment cool down and maintained exhaust temperatures above the SCR activity threshold for a longer duration.
Herb-induced hepatitis secondary to artemisinin: A case report
Authors: Zhan Jiwei , Ding Meilin , Li Jin , Su Lei
Published: October 2022

This report describes a rare case of severe liver injury secondary to a herbal supplement containing artemisinin. The patient received plasma exchange with bilirubin filtration adsorption therapy. The case is unique in its severe cholestasis. Bilirubin decreased to baseline after 62 days. This will help to improve clinicians' awareness of the diagnosis and treatment of drug-induced liver injury.
Micro-Raman spectroscopy study of optically trapped erythrocytes in malaria, dengue and leptospirosis infections
Authors: Jacob Sanu Susan , Lukose Jijo , Bankapur Aseefhali , Mithun N. , Vani Lakshmi R. , Acharya Mahendra , Rao Pragna , Kamath Asha , Baby Prathap M. , Rao Raghavendra K. , Chidangil Santhosh
Published: October 2022

Malaria, dengue and leptospirosis are three tropical infectious diseases that present with severe hematological derangement causing significant morbidity and mortality, especially during the seasonal monsoons. During the course of these infectious diseases, circulating red blood cells are imperiled to the direct ill-effects of the infectious pathogen in the body as well as to the pro-inflammatory cytokines generated as a consequence of the infection. RBCs when exposed to such inflammatory and/or pathogenic milieu are susceptible to injuries such as RBC programmed eryptosis or RBC programmed necrosis. This research aimed to explore the Raman spectra of live red cells that were extracted from patients infected with malaria, dengue, and leptospirosis. Red cells were optically trapped and micro-Raman probed using a 785 nm Diode laser. RBCs from samples of all three diseases displayed Raman signatures that were significantly altered from the normal/healthy. Distinct spectral markers that were common across all the four groups were obtained from various standardized multivariate analytical methods. Following comprehensive examination of multiple studies, we propose these spectral wavenumbers as “Raman markers of RBC injury.” Findings in our study display that anemia-triggering infections can inflict variations in the healthy status of red cells, easily identifiable by selectively analyzing specific Raman markers. Additionally, this study also highlights relevant statistical tools that can be utilized to study Raman spectral data from biological samples which could help identify the very significant Raman peaks from the spectral band. This approach of RBC analysis can foster a better understanding of red cell behavior and their alterations exhibited in health and disease.
Targeting acid ceramidase ameliorates fibrosis in mouse models of non-alcoholic steatohepatitis
Authors: Yu Amy , Cable Carson , Sharma Sachin , Shihan Mahbubul H. , Mattis Aras N. , Mileva Izolda , Hannun Yusuf A. , Duwaerts Caroline C. , Chen Jennifer Y.
Published: October 2022

Non-alcoholic fatty liver disease (NAFLD) is a common cause of liver disease worldwide, and is characterized by the accumulation of fat in the liver. Non-alcoholic steatohepatitis (NASH), an advanced form of NAFLD, is a leading cause of liver transplantation. Fibrosis is the histologic feature most associated with liver-related morbidity and mortality in patients with NASH, and treatment options remain limited. In previous studies, we discovered that acid ceramidase (aCDase) is a potent antifibrotic target using human hepatic stellate cells (HSCs) and models of hepatic fibrogenesis. Using two dietary mouse models, we demonstrate that depletion of aCDase in HSC reduces fibrosis without worsening metabolic features of NASH, including steatosis, inflammation, and insulin resistance. Consistently, pharmacologic inhibition of aCDase ameliorates fibrosis but does not alter metabolic parameters. The findings suggest that targeting aCDase is a viable therapeutic option to reduce fibrosis in patients with NASH.
Comparing the efficacy of different antibiotic regimens on osteomyelitis: A network meta-analysis of animal studies
Authors: Shi Xiangwen , Wu Yipeng , Ni Haonan , Chen Xi , Xu Yongqing
Published: October 2022

Background

Despite the surge in the number of antibiotics used to treat preclinical osteomyelitis (OM), their efficacy remains inadequately assessed.

Objective

To establish network comparisons on the efficacy of antibiotic regimens on OM in animal studies.

Methods

PubMed, Embase, Web of Science, and The Cochrane Library were searched from inception to March 2022 for relevant articles. Odds ratios (ORs) were generated for dichotomous variants, and the standard mean difference (SMD) was calculated for constant variables. The predominant outcomes were the effective rate of sterility, also known as sterility rates, as well as the bacterial counts at the end of the experiments and antibiotic concentrations in serum or bone. All the network meta-analyses were performed using STATA MP 16.0. This study was registered in the International Prospective Register of Systematic Reviews (PROSPERO; no. CRD42022316544).

Results

A total of 28 eligible studies with 1,488 animals were included for data analysis, including 13 antibiotic regimens. Regarding the effective rate of sterility, glycopeptides (GLY), linezolid (LIN), rifampicin (RIF)+β-Lactam, and β-Lactam showed significant efficacy compared with placebo (OR ranging from 0.01 to 0.08). For radiological grade, only RIF+GLY (SMD: −5.92, 95%CI: −11.65 to −0.19) showed significant efficacy compared with placebo. As for reducing bacteria count, fosfomycin (FOS), tigecycline (TIG), GLY, LIN, RIF, RIF+β-Lactam, RIF+GLY, aminoglycosides (AMI), and clindamycin (CLI) showed significant efficacy compared with placebo (SMD ranging from −6.32 to −2.62). Moreover, the bone concentrations of GLY were higher 1 h after administration and the higher blood concentrations were higher after 1 h and 4 h compared with the other antibiotics.

Conclusion

Multiple antibiotic regimens showed significant efficacy in animals with OM, including increasing effective rates of sterility, reducing bacterial counts, and lowering radiological scores. Among them, RIF+GLY was the most promising treatment regimen owing to its optimal efficacy. Based on the preclinical studies included in our meta-analysis, head-to-head clinical randomized controlled trials are required to confirm these findings in humans.
Validation of baking as a kill-step for controlling Shiga toxin-producing Escherichia coli during traditional crust pizza baking process
Authors: Singh Arshdeep , Channaiah Lakshmikantha H.
Published: October 2022

A study was conducted to validate a simulated traditional crust pepperoni pizza baking process to control Shiga toxin-producing Escherichia coli (STEC) and to determine the heat resistance characteristics of STEC in pizza dough. Pizza dough and pepperoni slices were inoculated with 7 strains STEC cocktail and baked at 500°F (260°C) for 12 min using a conventional kitchen oven followed by 15 min of ambient air cooling. The mean internal temperature of the pizza reached 209.32 ± 1.94°F by the end of 12 min of baking and dropped to 137.90 ± 2.88°F after the 15 min ambient air cooling. The aw and pH of the traditional crust pizza did not alter significantly during the baking process. The STEC population decreased by >5 log CFU/g in traditional crust pizza after 12 min of baking. Where pepperoni slices were used as a source of STEC introduction, a reduction of >6.5 log CFU/g was observed. The D-values of STEC cocktail in pizza dough at 55, 58, 61°C were 49.5 ± 4.10, 15.3 ± 0.68, and 2.8 ± 0.31 min, respectively. The z-value of STEC was 4.8 ± 0.16°C. This study validated that a typical traditional crust pizza baking process with ~209°F internal temperature for at least 12 min will result in 5 log reductions in STEC population.
Neutrophil-to-lymphocyte ratio as a potential biomarker in predicting influenza susceptibility
Authors: Wang Guoyun , Lv Cheng , Liu Cheng , Shen Wenjun
Published: October 2022

Background

Human population exposed to influenza viruses exhibited wide variation in susceptibility. The ratio of neutrophils to lymphocytes (NLR) has been examined to be a marker of systemic inflammation. We sought to investigate the relationship between influenza susceptibility and the NLR taken before influenza virus infection.

Methods

We investigated blood samples from five independent influenza challenge cohorts prior to influenza inoculation at the cellular level by using digital cytometry. We used multi-cohort gene expression analysis to compare the NLR between the symptomatic infected (SI) and asymptomatic uninfected (AU) subjects. We then used a network analysis approach to identify host factors associated with NLR and influenza susceptibility.

Results

The baseline NLR was significantly higher in the SI group in both discovery and validation cohorts. The NLR achieved an AUC of 0.724 on the H3N2 data, and 0.736 on the H1N1 data in predicting influenza susceptibility. We identified four key modules that were not only significantly correlated with the baseline NLR, but also differentially expressed between the SI and AU groups. Genes within these four modules were enriched in pathways involved in B cell-mediated immune responses, cellular metabolism, cell cycle, and signal transduction, respectively.

Conclusions

This study identified the NLR as a potential biomarker for predicting disease susceptibility to symptomatic influenza. An elevated NLR was detected in susceptible hosts, who may have defects in B cell-mediated immunity or impaired function in cellular metabolism, cell cycle or signal transduction. Our work can serve as a comparative model to provide insights into the COVID-19 susceptibility.
The transmembrane replacement H7N9-VLP vaccine displays high levels of protection in mice
Authors: Qin Jianru , Hu Bing , Song Qiqi , Wang Ruijuan , Zhang Xiangfei , Yu Yaqi , Wang Jian-Hua
Published: October 2022

The incidence of infections caused by the H7N9 subtype of the influenza virus has expanded rapidly in China in recent decades, generating massive economic loss and posing a significant threat to public health. In the absence of specialized antiviral treatments or long-term effective preventative vaccinations, it is critical to constantly enhance vaccines and create effective antiviral drugs to prevent the recurrence of pandemics. In the present study, a transmembrane-substituted (TM) virus-like particle (VLP)-based vaccine was created by replacing the transmembrane region of hemagglutinin (HA) protein with the transmembrane region of the H3 HA protein and then used to immunize BALB/c mice. Sera and T cells were collected from the immunized mice to evaluate the passive immune effects. Our results showed that naïve mice achieved 80–100% protection against homologous and heterologous H7N9 influenza strains after receiving passive serum immunization; the protective effect of the TM VLPs was more evident than that of the wild-type HA VLPs. In contrast, mice immunized with passive T cells achieved only 20 to 80% protection against homologous or heterologous strains. Our findings significantly contribute to understanding the control of the H7N9 virus and the development of a vaccine.
Phage-resistant Pseudomonas aeruginosa against a novel lytic phage JJ01 exhibits hypersensitivity to colistin and reduces biofilm production
Authors: Wannasrichan Wichanan , Htoo Htut Htut , Suwansaeng Rubsadej , Pogliano Joe , Nonejuie Poochit , Chaikeeratisak Vorrapon
Published: October 2022

Pseudomonas aeruginosa, a major cause of nosocomial infections, has been categorized by World Health Organization as a critical pathogen urgently in need of effective therapies. Bacteriophages or phages, which are viruses that specifically kill bacteria, have been considered as alternative agents for the treatment of bacterial infections. Here, we discovered a lytic phage targeting P. aeruginosa, designated as JJ01, which was classified as a member of the Myoviridae family due to the presence of an icosahedral capsid and a contractile tail under TEM. Phage JJ01 requires at least 10 min for 90% of its particles to be adsorbed to the host cells and has a latent period of 30 min inside the host cell for its replication. JJ01 has a relatively large burst size, which releases approximately 109 particles/cell at the end of its lytic life cycle. The phage can withstand a wide range of pH values (3–10) and temperatures (4–60°C). Genome analysis showed that JJ01 possesses a complete genome of 66,346 base pairs with 55.7% of GC content, phylogenetically belonging to the genus Pbunavirus. Genome annotation further revealed that the genome encodes 92 open reading frames (ORFs) with 38 functionally predictable genes, and it contains neither tRNA nor toxin genes, such as drug-resistant or lysogenic-associated genes. Phage JJ01 is highly effective in suppressing bacterial cell growth for 12 h and eradicating biofilms established by the bacteria. Even though JJ01-resistant bacteria have emerged, the ability of phage resistance comes with the expense of the bacterial fitness cost. Some resistant strains were found to produce less biofilm and grow slower than the wild-type strain. Among the resistant isolates, the resistant strain W10 which notably loses its physiological fitness becomes eight times more susceptible to colistin and has its cell membrane compromised, compared to the wild type. Altogether, our data revealed the potential of phage JJ01 as a candidate for phage therapy against P. aeruginosa and further supports that even though the use of phages would subsequently lead to the emergence of phage-resistant bacteria, an evolutionary trade-off would make them more sensitive to antibiotics.
Molecular identification, antifungal susceptibility, and resistance mechanisms of pathogenic yeasts from the China antifungal resistance surveillance trial (CARST-fungi) study
Authors: Wang Qiqi , Cai Xuan , Li Yun , Zhao Jianhong , Liu Zhiyong , Jiang Yan , Meng Ling , Li Yanming , Pan Shiyang , Ai Xiaoman , Zhang Fang , Li Ruoyu , Zheng Bo , Wan Zhe , Liu Wei
Published: October 2022

To have a comprehensive understanding of epidemiology and antifungal susceptibilities in pathogenic yeasts, the China Antifungal Resistance Surveillance Trial (CARST-fungi) study was conducted. All yeast isolates were identified by ribosomal DNA sequencing. Antifungal susceptibilities were performed using CLSI M27-A4 broth microdilution method. Sequence and expression level of resistant-related genes in resistant/non-wide-type (NWT) Candida isolates were analyzed. Totally 269 nonduplicate yeast isolates from 261 patients were collected. About half of the yeast isolates (127, 47.2%) were recovered from blood, followed by ascetic fluid (46, 17.1%). C. albicans remained the most prevalent (120, 44.6%), followed by C. parapsilosis complex (50, 18.6%), C. tropicalis (40, 14.9%), and C. glabrata (36, 13.4%). Fourteen (11.7%) C. albicans isolates and 1 (2.0%) C. parapsilosis isolate were resistant/NWT to triazoles. Only 42.5% (17/40) C. tropicalis were susceptible/WT to all the triazoles, with 19 (47.5%) isolates NWT to posaconazole and 8 (20%) cross-resistant to triazoles. Among C. glabrata, 20 (55.6%) and 8 (22.2%) isolates were resistant/NWT to voriconazole and posaconazole, respectively, and 4 (10.3%) isolates were cross-resistant to triazoles. Isavuconazole was the most active triazole against common Candida isolates. Except for 2 isolates of C. glabrata cross-resistant to echinocandins which were also NWT to POS and defined as multidrug-resistant, echinocandins exhibit good activity against common Candida species. All isolates were WT to AMB. For less common species, Rhodotorula mucilaginosa exhibited high MICs to echinocandins and FLC, and 1 isolate of Trichosporon asahii showed high MICs to all the antifungals except AMB. Among triazole-resistant Candida isolates, ERG11 mutations were detected in 10/14 C. albicans and 6/23 C. tropicalis, while 21/23 C. tropicalis showed MDR1 overexpression. Overexpression of CDR1, CDR2, and SNQ2 exhibited in 14, 13, and 8 of 25 triazole-resistant C. glabrata isolates, with 5 isolates harboring PDR1 mutations and 2 echinocandins-resistant isolates harboring S663P mutation in FKS2. Overall, the CARST-fungi study demonstrated that although C. albicans remain the most predominant species, non-C. albicans species accounted for a high proportion. Triazole-resistance is notable among C. tropicalis and C. glabrata. Multidrug-resistant isolates of C. glabrata and less common yeast have been emerging.
Role and potentialities of bacteria associated with Tuber magnatum: A mini-review
Authors: Monaco Pamela , Naclerio Gino , Mello Antonietta , Bucci Antonio
Published: October 2022

Among the hypogeous ectomycorrhizal fungi, the white truffle Tuber magnatum Picco is the species of greatest interest, both from an ecological and economic point of view. The increasing market demand of the precious white truffle along with the fall in its natural production led to a growing interest in cultivation techniques and encouraged truffle growers and researchers to deeper investigate factors that could affect and improve T. magnatum productivity. In this context, microbial communities play a central role. Indeed, in the last few years, the hypothesis of a potential link between microbial community composition and truffle orchard productivity is arousing a greater attention. Moreover, since the value of the prized T. magnatum can vary in relation to its provenience, the need to define a reliable tracking system is also emerging and bacteria appear to be a promising tool. Accordingly, the present mini-review summarises the knowledge currently available on T. magnatum microbial communities, focusing on the role of truffle-associated bacteria and highlighting similarities and differences between samples of different origin, to address the following issues: (i) Is there a correlation between microbial taxa and truffle ground productivity? (ii) Can bacteria actually be used as markers of T. magnatum geographic origin? The identification of microorganisms able to promote T. magnatum formation may represent an important advance in the field of truffle farming. Similarly, the detection of bacterial taxa that can be used as markers of T. magnatum origin could have a considerable impact on truffle industry and trade, even at local scale.
Antimicrobial susceptibility to polymyxin B and other comparators against Gram-negative bacteria isolated from bloodstream infections in China: Results from CARVIS-NET program
Authors: Xi Jingyuan , Jia Peiyao , Zhu Ying , Yu Wei , Zhang Jingjia , Gao Haotian , Kang Wei , Zhang Ge , Li Jin , Wang Tong , Xu Yingchun , Yang Qiwen
Published: October 2022

Objective

To investigate the bacterial distribution and antimicrobial resistance profile of clinical isolates from Gram-negative bacteria bloodstream infections (GNBSI) in China.

Methods

The clinical bacterial strains isolated from blood culture were collected during April 2019 to December 2021 in 21 member hospitals of China Bloodstream Gram-negative Pathogens Antimicrobial Resistance and Virulence Surveillance Network (CARVIS-NET). Antibiotic susceptibility test was conducted by broth microdilution method recommended by Clinical and Laboratory Standards Institute (CLSI, United States). WHONET 2021 and SPSS 22.0 were used to analyze data.

Results

During the study period, 1939 Gram-negative bacteria were collected from 21 hospitals, among which 1,724 (88.9%) were Enterobacteriaceae, 207 (10.7%) were non-fermenting Gram-negative bacteria and 8 (0.4%) were others. The top five bacterial species were Escherichia coli (46.2%), Klebsiella pneumoniae (31.6%), Pseudomonas aeruginosa (4.9%), Acinetobacter baumannii (4.2%) and Enterobacter cloacae (3.0%). For K. pneumoniae, antibiotic resistance was mainly prevalent in hospital-associated bloodstream infections, while for A. baumannii, antibiotic resistance was mainly prevalent in community-associated bloodstream infections. It is worth mentioning that 94.1% of the 1939 Gram-negative isolates were susceptible to polymyxin B. The sensitivity of the strains involved in our investigation to polymyxin B is highly correlated with their sensitivity to colistin.

Conclusion

The surveillance results in CARVIS-NET-2021 showed that the main pathogens of GNBSI in China were Enterobacteriaceae, while E. coli was the most common pathogen. The resistance rates of K. pneumonia, P. aeruginosa, A. baumannii, and E. cloacae to multiple antibiotics kept on a high level. In many cases, polymyxin B and colistin has become the last-resort agents to combat bloodstream infections caused by multidrug-resistant (MDR) Gram-negative bacteria.
Assessment of the immunogenicity and protection of a Nipah virus soluble G vaccine candidate in mice and pigs
Authors: Gao Zihan , Li Tao , Han Jicheng , Feng Sheng , Li Letian , Jiang Yuhang , Xu Zhiqiang , Hao Pengfei , Chen Jing , Hao Jiayi , Xu Peng , Tian Mingyao , Jin Ningyi , Huang Weijin , Li Chang
Published: October 2022

Nipah virus (NiV) is a newly emerged extremely dangerous zoonotic pathogen highly fatal to humans. Currently, no approved vaccine is available against NiV. This study employed a mammalian eukaryotic system to express NiV soluble G glycoprotein (NiV-sG), using CpG oligodeoxynucleotides (CpG)/Aluminum salt (Alum) as adjuvants to obtain a recombinant subunit vaccine candidate. We also evaluated the immunogenicity and efficacy of the protein in mice and pigs. The results showed that humoral and cellular immune responses were induced in all the vaccination groups in two animal models. The levels of specific and neutralizing antibodies and the proliferation levels of T helper(Th) cells were significantly higher than those in the control group. The protective efficacy of the subunit vaccines evaluated in the pseudovirus in vivo infection mouse model strongly suggested that this vaccine could provide protective immunity against NiV. A neoadjuvant (HTa) based on liposomes and cholera toxin combined with CpG/Alum was exploited and evaluated in mice. The neoadjuvant group showed a more protective efficacy than the CpG/Alum group. The aforementioned results indicated that the subunit vaccine could be used as a promising candidate vaccine for preventing Nipah virus infection.
Development of an AAV DNA-based synthetic vector for the potential gene therapy of hemophilia in children
Authors: Shoti Jakob , Qing Keyun , Srivastava Arun
Published: October 2022

Recombinant AAV serotype vectors and their variants have been or are currently being used for gene therapy for hemophilia in several phase I/II/III clinical trials in humans. However, none of these trials have included children with hemophilia since the traditional liver-directed AAV gene therapy will not work in these patients because of the following reasons: (i) Up until age 10–12, the liver is still growing and dividing, and with every cell division, the AAV vector genomes will be diluted out due to their episomal nature; and (ii) Repeated gene delivery will be needed, but repeat dosing, even with an ideal AAV vector is not an option because of pre-existing antibodies to AAV vectors following the first administration. Here we describe the development of an optimized human Factor IX (hF.IX) gene expression cassette under the control of a human liver-specific transthyretin promoter covalently flanked by AAV inverted terminal repeats (ITRs) with no open ends (optNE-TTR-hF.IX), which mediated ~sixfold higher hF.IX levels than that from a linear TTR-hF.IX DNA construct in human hepatoma cells up to four-weeks post-transfection. In future studies, encapsidation of the optNE-TTR-hF.IX DNA in liver-targeted synthetic liposomes, may provide a viable approach for the potential gene therapy for hemophilia in children.
The spatial distribution and biogeochemical drivers of nitrogen cycle genes in an Antarctic desert
Authors: Pascoal Francisco , Areosa Inês , Torgo Luís , Branco Paula , Baptista Mafalda S. , Lee Charles K. , Cary S. Craig , Magalhães Catarina
Published: October 2022

Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.
Deterministic processes shape bacterial community assembly in a karst river across dry and wet seasons
Authors: Wu Yongjie , Zhang Yang , Yang Xueqin , Li Kaiming , Mai Bixian , He Zhili , Wu Renren
Published: October 2022

Karst rivers are particularly vulnerable to bacterial pollution because immigrations are easily diffused from the surrounding environments due to their strong hydraulic connectivity. However, the assembly mechanism in shaping riverine bacterial biogeography is still poorly understood, especially for an ecosystem in the karst area. Here, 16S rRNA genes were used to explore the spatiotemporal and biogeographical patterns of bacterial communities from the Chishui River in the dry and wet seasons, and explore the impact of external immigration on the assembly of water bacterial communities. Our results showed clear spatiotemporal patterns of bacterial communities with a more pronounced seasonal rather than spatial fluctuation, which appeared to be dependent on seasonal-related environmental factors (e.g., temperature and turbidity). The bacterial communities exhibited a significant (p < 0.05) distance–decay pattern in both seasons, and they had a stronger distance–decay relationship in the dry season than in the wet season. However, most of the biomarkers of different external immigrations did not show significant (p > 0.05) distance–decay patterns along the Chishui river, implying that the biomarkers could be used as indicators of external immigration (e.g., OTU_125 and OTU_536). Also, the tributaries were the main external immigration (20.44–83.68%) for the Chishui River, while other terrestrial immigration (e.g., livestock, the soil of the cropland, brewing wastewater treatment plant, and sewages) showed relatively little influence, which could be due to the hydrodynamic conditions (e.g., fragile rock–soil system and hydrological structure) of the karst river. Additionally, the assembly of water bacterial communities in the Chishui river was governed by more determinism (50.7–85.7%) than stochasticity (14.3–49.3%) in both the dry and wet seasons. We demonstrated that the bacterial community’s substantial variations are largely shaped by deterministic processes, thereby providing a better understanding of spatiotemporal patterns and mechanisms of the bacterial community in karst river waters.
Stochastic factors drive dynamics of ammonia-oxidizing archaeal and bacterial communities in aquaculture pond sediment
Authors: Dai Lili , Yu Liqin , Peng Liang , Tao Ling , Liu Yanbin , Li Gu
Published: October 2022

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in nitrification, which is essential in the global nitrogen cycle. However, their dynamics and the underlying community processes in agricultural ecosystems under disturbance remain largely unknown. In this study we examined the spatiotemporal dynamics of AOA and AOB communities and analyzed their community processes in the sediment of aquaculture ponds across three different areas in China. We found some significant temporal changes in AOA and AOB community diversity and abundances, but no temporal changes in community composition, despite the significant variations in sediment properties between different sampling times. Nevertheless, significant differences were found for AOA and AOB communities between different areas. Distinct area-specific taxa were detected, and they were found to be important in determining the response of AOA and AOB communities to environmental factors. In addition, geographic distance was found to be significantly correlated with AOA and AOB community composition, which demonstrates that dispersal limitation could significantly contribute to the variations in AOA and AOB communities, and stochastic processes were found to be important in structuring AOA/AOB communities in aquaculture ponds. Taken together, our study indicates that the dynamics of AOA and AOB are based on their community characteristics in aquaculture pond sediment. Our results, for the first time, provide evidence for the dynamics of AOA and AOB communities being driven by stochastic factors in a disturbed environment, and might also be of use in the management of the aquaculture environment.
Screening of cellulose-degrading yeast and evaluation of its potential for degradation of coconut oil cake
Authors: Fu Zi-huan , Liu Jing , Zhong Long-bin , Huang Huan , Zhu Peng , Wang Cai-xing , Bai Xin-peng
Published: October 2022

Coconut oil cake (COC), a byproduct of oil extraction, contains high levels of cellulose. The aim of this study was to isolate a cellulose-degrading yeast from rotten dahlia that can effectively use COC as the only carbon source for cellulase secretion. Based on screening, Meyerozyma guillermondii CBS 2030 (M. guillermondii) was identified as a potential candidate, with the highest cellulolytic activity among the yeast strains isolated, with the carboxymethyl cellulase (CMCase) activity reaching 102.96 U/mL on day 5. The cellulose in COC samples was evaluated before and after degradation by M. guillermondii. Analysis based on field emission scanning electron microscopy (FESEM) revealed that the COC structure was changed significantly during the treatment, indicating effective hydrolysis. Fourier transform infrared spectroscopy (FTIR) of the modified functional groups indicated successful depolymerization of coconut cake. X-ray diffraction (XRD) and analysis of color differences established effective degradation of COC by M. guillermondii. The results demonstrate that M. guillermondii effectively secretes CMCase and degrades cellulose, which has important practical significance in COC degradation.
Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C
Authors: Chi Yi , Shi Jenny , Xing Dong , Tan Longzhi
Published: October 2022

The three-dimensional (3D) structure of chromosomes influences essential biological processes such as gene expression, genome replication, and DNA damage repair and has been implicated in many developmental and degenerative diseases. In the past two centuries, two complementary genres of technology—microscopy, such as fluorescence in situ hybridization (FISH), and biochemistry, such as chromosome conformation capture (3C or Hi-C)—have revealed general principles of chromosome folding in the cell nucleus. However, the extraordinary complexity and cell-to-cell variability of the chromosome structure necessitate new tools with genome-wide coverage and single-cell precision. In the past decade, single-cell Hi-C emerges as a new approach that builds upon yet conceptually differs from bulk Hi-C assays. Instead of measuring population-averaged statistical properties of chromosome folding, single-cell Hi-C works as a proximity-based “biochemical microscope” that measures actual 3D structures of individual genomes, revealing features hidden in bulk Hi-C such as radial organization, multi-way interactions, and chromosome intermingling. Single-cell Hi-C has been used to study highly dynamic processes such as the cell cycle, cell-type-specific chromosome architecture (“structure types”), and structure–expression interplay, deepening our understanding of DNA organization and function.
A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations
Authors: Martin Juliette , Frezza Elisa
Published: October 2022

Protein-protein interactions are at the basis of many protein functions, and the knowledge of 3D structures of protein-protein complexes provides structural, mechanical and dynamical pieces of information essential to understand these functions. Protein-protein interfaces can be seen as stable, organized regions where residues from different partners form non-covalent interactions that are responsible for interaction specificity and strength. They are commonly described as a peripheral region, whose role is to protect the core region that concentrates the most contributing interactions, from the solvent. To get insights into the dynamics of protein-protein complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on eight different protein-protein complexes of different functional class and interface size by taking into account the bound and unbound forms. On the one hand, we characterized structural changes upon binding of the proteins, and on the other hand we extensively analyzed the interfaces and the structural waters involved in the binding. Based on our analysis, in 6 cases out of 8, the interfaces rearranged during the simulation time, in stable and long-lived substates with alternative residue-residue contacts. These rearrangements are not restricted to side-chain fluctuations in the periphery but also affect the core interface. Finally, the analysis of the waters at the interface and involved in the binding pointed out the importance to take into account their role in the estimation of the interaction strength.
pyDockDNA: A new web server for energy-based protein-DNA docking and scoring
Authors: Rodríguez-Lumbreras Luis Angel , Jiménez-García Brian , Giménez-Santamarina Silvia , Fernández-Recio Juan
Published: October 2022

Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure. We present here the pyDockDNA web server, which can successfully model a protein-DNA complex with a reasonable predictive success rate (as benchmarked on a standard dataset of protein-DNA complex structures, where DNA is in B-DNA conformation). The server implements the pyDockDNA program, as a module of pyDock suite, thus including third-party programs, modules, and previously developed tools, as well as new modules and parameters to handle the DNA properly. The user is asked to enter Protein Data Bank files for protein and DNA input structures (or suitable models) and select the chains to be docked. The server calculations are mainly divided into three steps: sampling by FTDOCK, scoring with new energy-based parameters and the possibility of applying external restraints. The user can select different options for these steps. The final output screen shows a 3D representation of the top 10 models and a table sorting the model according to the scoring function selected previously. All these output files can be downloaded, including the top 100 models predicted by pyDockDNA. The server can be freely accessed for academic use (https://model3dbio.csic.es/pydockdna).