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The Impact of Excluding Adverse Neonatal Outcomes on the Creation of Gestational Weight Gain Charts Among Women from Low- and Middle-income Countries with Normal and Overweight BMI

Rangel Bousquet Carrilho T, Wang D, Hutcheon JA, Wang M, Fawzi WW, Kac G, et al.

Am J Clin Nutr, 2024 Mar 22.
PMID: 38522618 DOI: 10.1016/j.ajcnut.2024.03.016

BACKGROUND: Existing gestational weight gain (GWG) charts vary considerably in their choice of exclusion/inclusion criteria, and it is unclear to what extent these criteria create differences in the charts' percentile values.
OBJECTIVES: We aimed to establish the impact of including/excluding pregnancies with adverse neonatal outcomes when constructing GWG charts.
METHODS: This is an individual participant data analysis from 31 studies from low- and middle-income countries. We created a dataset that included all participants and a dataset restricted to those with no adverse neonatal outcomes: preterm < 37 wk, small or large for gestational age, low birth weight < 2500 g, or macrosomia > 4000 g. Quantile regression models were used to create GWG curves from 9 to 40 wk, stratified by prepregnancy BMI, in each dataset.
RESULTS: The dataset without the exclusion criteria applied included 14,685 individuals with normal weight and 4831 with overweight. After removing adverse neonatal outcomes, 10,479 individuals with normal weight and 3466 individuals with overweight remained. GWG distributions at 13, 27, and 40 wk were virtually identical between the datasets with and without the exclusion criteria, except at 40 wk for normal weight and 27 wk for overweight. For the 10th and 90th percentiles, the differences between the estimated GWG were larger for overweight (∼1.5 kg) compared with normal weight (<1 kg). Removal of adverse neonatal outcomes had minimal impact on GWG trajectories of normal weight. For overweight, the percentiles estimated in the dataset without the criteria were slightly higher than those in the dataset with the criteria applied. Nevertheless, differences were <1 kg and virtually nonexistent at the end of pregnancy.
CONCLUSIONS: Removing pregnancies with adverse neonatal outcomes has little or no influence on the GWG trajectories of individuals with normal and overweight.
Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.

Autophagy, 2016;12(1):1-222.
PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
Fulltext The Typical Damage Form and Mechanism of a Railway Prestressed Concrete Sleeper

You R, Wang J, Ning N, Wang M, Zhang J

Materials (Basel), 2022 Nov 15;15(22).
PMID: 36431559 DOI: 10.3390/ma15228074

Prestressed concrete sleepers are an important track component that is widely used in railway ballast track. Prestressed concrete sleepers have high strength, strong stability, and good durability; thus, their operation and use in railways are beneficial. However, in different countries and regions, certain damage to sleepers typically appears. Existing research on concrete sleepers focuses primarily on the structural design method, the application of new materials, theoretical analysis, and bearing strength test research, while ignoring sleeper damage. There are a few sleeper damage studies, but they look at only one type of damage; thus, there is no comprehensive study of prestressed concrete sleeper damage. The damage forms of prestressed concrete sleeper damage are thus summarized in this study, and the theory of the causes of prestressed concrete sleepers is analyzed based on the limit state method for the first time. The findings indicate that sleeper structure design is the primary cause of its operation and use status, and that special measures should be considered based on sleeper use conditions. In addition to meeting design requirements, materials, curing systems, product inspection, and other factors must be considered during manufacturing to improve the sleepers' long-term performance. Keeping the track in good condition, including but not limited to the state of fasteners, ballast bed, and track geometry is also an important aspect of preventing sleeper damage. The outcomes of this study provide better insights into the influences of damage to railway prestressed concrete sleepers and can be used to improve track maintenance and inspection criteria.
Phylogeography of Tetrancistrum nebulosi (Monogenea, Dactylogyridae) on the host of mottled spinefoot (Siganus fuscescens) in the South China Sea, inferred from mitochondrial COI and ND2 genes

Wang M, Yan S, Brown CL, Shaharom-Harrison F, Shi SF, Yang TB

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3865-3875.
PMID: 25319302

To examine the phylogeographical pattern of Tetrancistrum nebulosi (Monogenea, Dactylogyridae) in the South China Sea, fragments of mitochondrial cytochrome c oxidase subunit I and NADH dehydrogenase subunit 2 genes were obtained for 220 individuals collected from 8 localities along the southeast coast of China and 1 locality in Terengganu, Malaysia. Based on these two genes, two and three distinct clades with geographic signals were revealed on the phylogenetic trees respectively. The divergence between these clades was estimated to occur in the late Pleistocene. Analysis of molecular variance and pairwise FSTsuggested a high rate of gene flow among individuals sampled from the Chinese coast, but with obvious genetic differentiation from the Malaysian population. Mismatch distribution and neutrality tests indicated that the T. nebulosi population experienced expansion in Pleistocene low sea level periods. Vicariance was considered to account for the genetic divergence between Chinese and Malaysian populations, while sea level fluctuations and mainland-island connections during glacial cycles were associated with the slight genetic divergence between the populations along the mainland coast of China and those off Sanya. On the contrary, oceanographic circulations and host migration could lead to genetic homogeneity of populations distributed along the mainland coast of China.
Measurement of WZ and ZZ production in pp collisions at [Formula: see text] in final states with b-tagged jets

CMS Collaboration, Chatrchyan S, Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, et al.

Eur Phys J C Part Fields, 2014 08 07;74(8):2973.
PMID: 25814904

Measurements are reported of the WZ and ZZ production cross sections in proton-proton collisions at [Formula: see text][Formula: see text] in final states where one Z boson decays to b-tagged jets. The other gauge boson, either W or Z, is detected through its leptonic decay (either [Formula: see text], [Formula: see text] or [Formula: see text], [Formula: see text], or [Formula: see text]). The results are based on data corresponding to an integrated luminosity of 18.9 fb[Formula: see text] collected with the CMS detector at the Large Hadron Collider. The measured cross sections, [Formula: see text] and [Formula: see text], are consistent with next-to-leading order quantum chromodynamics calculations.
Measurement of jet multiplicity distributions in [Formula: see text] production in pp collisions at [Formula: see text]

CMS Collaboration, Chatrchyan S, Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, et al.

Eur Phys J C Part Fields, 2014 08 20;74(8):3014.
PMID: 25814909

The normalised differential top quark-antiquark production cross section is measured as a function of the jet multiplicity in proton-proton collisions at a centre-of-mass energy of 7[Formula: see text] at the LHC with the CMS detector. The measurement is performed in both the dilepton and lepton+jets decay channels using data corresponding to an integrated luminosity of 5.0[Formula: see text]. Using a procedure to associate jets to decay products of the top quarks, the differential cross section of the [Formula: see text] production is determined as a function of the additional jet multiplicity in the lepton+jets channel. Furthermore, the fraction of events with no additional jets is measured in the dilepton channel, as a function of the threshold on the jet transverse momentum. The measurements are compared with predictions from perturbative quantum chromodynamics and no significant deviations are observed.
Fulltext Search for direct pair production of supersymmetric partners to the τ lepton in proton-proton collisions at s = 13 TeV

CMS Collaboration, Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, et al.

Eur Phys J C Part Fields, 2020;80(3):189.
PMID: 32226948 DOI: 10.1140/epjc/s10052-020-7739-7

A search is presented for τ slepton pairs produced in proton-proton collisions at a center-of-mass energy of 13 TeV . The search is carried out in events containing two τ leptons in the final state, on the assumption that each τ slepton decays primarily to a τ lepton and a neutralino. Events are considered in which each τ lepton decays to one or more hadrons and a neutrino, or in which one of the τ leptons decays instead to an electron or a muon and two neutrinos. The data, collected with the CMS detector in 2016 and 2017, correspond to an integrated luminosity of 77.2 fb - 1 . The observed data are consistent with the standard model background expectation. The results are used to set 95% confidence level upper limits on the cross section for τ slepton pair production in various models for τ slepton masses between 90 and 200 GeV and neutralino masses of 1, 10, and 20 GeV . In the case of purely left-handed τ slepton production and decay to a τ lepton and a neutralino with a mass of 1 GeV , the strongest limit is obtained for a τ slepton mass of 125 GeV at a factor of 1.14 larger than the theoretical cross section.
Measurement of differential cross sections for the production of a pair of isolated photons in pp collisions at [Formula: see text]

CMS Collaboration, Chatrchyan S, Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, et al.

Eur Phys J C Part Fields, 2014 11 12;74(11):3129.
PMID: 25814874

A measurement of differential cross sections for the production of a pair of isolated photons in proton-proton collisions at [Formula: see text] is presented. The data sample corresponds to an integrated luminosity of 5.0[Formula: see text] collected with the CMS detector. A data-driven isolation template method is used to extract the prompt diphoton yield. The measured cross section for two isolated photons, with transverse energy above 40 and 25[Formula: see text] respectively, in the pseudorapidity range [Formula: see text], [Formula: see text] and with an angular separation [Formula: see text], is [Formula: see text][Formula: see text]. Differential cross sections are measured as a function of the diphoton invariant mass, the diphoton transverse momentum, the azimuthal angle difference between the two photons, and the cosine of the polar angle in the Collins-Soper reference frame of the diphoton system. The results are compared to theoretical predictions at leading, next-to-leading, and next-to-next-to-leading order in quantum chromodynamics.
Correlates of newly diagnosed HIV infection among cisgender women sex workers and transgender women sex workers in Greater Kuala Lumpur, Malaysia

Wang M, Lim SH, Gibson BA, Azwa I, Guadamuz TE, Altice FL, et al.

Int J STD AIDS, 2021 06;32(7):609-619.
PMID: 33752518 DOI: 10.1177/0956462420970417

Globally, cisgender women sex workers (CWSWs) and transgender women sex workers (TWSWs) experience increased vulnerabilities to HIV infection. Unfortunately, there is limited data on the drivers of HIV infection in these two understudied populations, particularly in Southeast Asia. To better understand factors associated with HIV infection, we evaluated correlates of newly diagnosed HIV infection in these two populations in Greater Kuala Lumpur, Malaysia. A total of 469 women (CWSW: n = 283; TWSW: n = 186) were included in this study. Most participants who tested HIV+ were unaware of their infection (59.6%; n = 34/57). Separate binary and multivariable logistic regressions were conducted to identify correlates of newly diagnosed HIV in CWSWs and TWSWs. Among CWSWs, Chlamydia trachomatis (aOR = 5.66; p = 0.007) and lifetime use of ecstasy/MDMA (aOR = 5.34; p = 0.03) were associated with newly diagnosed HIV, while condomless vaginal sex with clients was associated with lower likelihood of HIV infection (aOR = 0.98; p = 0.01). Among TWSWs, being single (aOR = 6.76; p = 0.03), using mobile application to solicit clients (aOR = 25.33; p = 0.006), and having C. trachomatis infection (aOR = 88.22, p = 0.02) were associated with newly diagnosed HIV. Expansion of HIV/sexually transmitted infection screening is needed to increase detection of HIV and linkage to care for sex workers. Interventions to reduce HIV infection among CWSWs and TWSWs should be tailored to these populations' unique vulnerabilities.
Fulltext Willingness to Use Pre-Exposure Prophylaxis (PrEP) for HIV Prevention and PrEP Implementation Preferences Among Transgender Women in Malaysia

Galka JM, Wang M, Azwa I, Gibson B, Lim SH, Shrestha R, et al.

Transgend Health, 2020 Dec;5(4):258-266.
PMID: 33644315 DOI: 10.1089/trgh.2020.0003

Introduction: Transgender women (TW) face one of the highest HIV burdens worldwide. In Malaysia, 12.4% of TW are HIV infected, ∼30-fold higher than in the Malaysian adult population. Pre-exposure prophylaxis (PrEP) is a highly effective HIV prevention strategy, however, little is known about TW's willingness to use PrEP or their preferences for receiving PrEP. This study examined the correlates of Malaysian TW's willingness to use PrEP and their attitudes and preferences related to delivery of PrEP and PrEP-related care. Methods: Between June and August 2017, 361 TW in Malaysia completed an online survey about their knowledge of and willingness to use PrEP for HIV prevention. Results: Only 20.2% of participants had ever previously heard of PrEP and none were currently taking PrEP. The majority (82.5%) expressed high willingness to take PrEP and most participants met the World Health Organization (WHO) indication for PrEP (82.3%). In the multivariate model, lifetime hormone use, prior postexposure prophylaxis use, and having completed a high school education were associated with higher willingness to use PrEP, while injection drug use, older age, and Chinese ethnicity were associated with lower PrEP willingness. Conclusion: TW in Malaysia are highly willing to use PrEP for HIV prevention. Differences in willingness to use PrEP identified by education, ethnicity, substance abuse, and age suggest different strategies may be needed to scale-up PrEP for this diverse community of TW.
Fulltext Air pollution and incidence of cancers of the stomach and the upper aerodigestive tract in the European Study of Cohorts for Air Pollution Effects (ESCAPE)

Nagel G, Stafoggia M, Pedersen M, Andersen ZJ, Galassi C, Munkenast J, et al.

Int J Cancer, 2018 10 01;143(7):1632-1643.
PMID: 29696642 DOI: 10.1002/ijc.31564

Air pollution has been classified as carcinogenic to humans. However, to date little is known about the relevance for cancers of the stomach and upper aerodigestive tract (UADT). We investigated the association of long-term exposure to ambient air pollution with incidence of gastric and UADT cancer in 11 European cohorts. Air pollution exposure was assigned by land-use regression models for particulate matter (PM) below 10 µm (PM10 ), below 2.5 µm (PM2.5 ), between 2.5 and 10 µm (PMcoarse ), PM2.5 absorbance and nitrogen oxides (NO2 and NOX ) as well as approximated by traffic indicators. Cox regression models with adjustment for potential confounders were used for cohort-specific analyses. Combined estimates were determined with random effects meta-analyses. During average follow-up of 14.1 years of 305,551 individuals, 744 incident cases of gastric cancer and 933 of UADT cancer occurred. The hazard ratio for an increase of 5 µg/m3 of PM2.5 was 1.38 (95% CI 0.99; 1.92) for gastric and 1.05 (95% CI 0.62; 1.77) for UADT cancers. No associations were found for any of the other exposures considered. Adjustment for additional confounders and restriction to study participants with stable addresses did not influence markedly the effect estimate for PM2.5 and gastric cancer. Higher estimated risks of gastric cancer associated with PM2.5 was found in men (HR 1.98 [1.30; 3.01]) as compared to women (HR 0.85 [0.5; 1.45]). This large multicentre cohort study shows an association between long-term exposure to PM2.5 and gastric cancer, but not UADT cancers, suggesting that air pollution may contribute to gastric cancer risk.
Fulltext Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria

Liu Y, Zheng K, Liu B, Liang Y, You S, Zhang W, et al.

Front Microbiol, 2021;12:726074.
PMID: 34512604 DOI: 10.3389/fmicb.2021.726074

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from -20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.
Fulltext Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster

Zhang W, Liang Y, Zheng K, Gu C, Liu Y, Wang Z, et al.

BMC Genomics, 2021 Sep 20;22(1):675.
PMID: 34544379 DOI: 10.1186/s12864-021-07978-4

BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.
RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.
CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.
Microenvironmental Interplay Predominated by Beneficial Aspergillus Abates Fungal Pathogen Incidence in Paddy Environment

Fan X, Matsumoto H, Wang Y, Hu Y, Liu Y, Fang H, et al.

Environ Sci Technol, 2019 Nov 19;53(22):13042-13052.
PMID: 31631659 DOI: 10.1021/acs.est.9b04616

Rice fungal pathogens, responsible for severe rice yield loss and biotoxin contamination, cause increasing concerns on environmental safety and public health. In the paddy environment, we observed that the asymptomatic rice phyllosphere microenvironment was dominated by an indigenous fungus, Aspergillus cvjetkovicii, which positively correlated with alleviated incidence of Magnaporthe oryzae, one of the most aggressive plant pathogens. Through the comparative metabolic profiling for the rice phyllosphere microenvironment, two metabolites were assigned as exclusively enriched metabolic markers in the asymptomatic phyllosphere and increased remarkably in a population-dependent manner with A. cvjetkovicii. These two metabolites evidenced to be produced by A. cvjetkovicii in either a phyllosphere microenvironment or artificial media were purified and identified as 2(3H)-benzofuranone and azulene, respectively, by gas chromatography coupled to triple quadrupole mass spectrometry and nuclear magnetic resonance analyses. Combining with bioassay analysis in vivo and in vitro, we found that 2(3H)-benzofuranone and azulene exerted dissimilar actions at the stage of infection-related development of M. oryzae. A. cvjetkovicii produced 2(3H)-benzofuranone at the early stage to suppress MoPer1 gene expression, leading to inhibited mycelial growth, while azulene produced lately was involved in blocking of appressorium formation by downregulation of MgRac1. More profoundly, the microenvironmental interplay dominated by A. cvjetkovicii significantly blocked M. oryzae epidemics in the paddy environment from 54.7 to 68.5% (p < 0.05). Our study first demonstrated implication of the microenvironmental interplay dominated by indigenous and beneficial fungus to ecological balance and safety of the paddy environment.
Fulltext Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus

Wang Z, Zhang F, Liang Y, Zheng K, Gu C, Zhang W, et al.

Microbiol Spectr, 2021 10 31;9(2):e0046321.
PMID: 34643440 DOI: 10.1128/Spectrum.00463-21

Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCE Alteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.
Spatiotemporal Dynamics of Coastal Viral Community Structure and Potential Biogeochemical Roles Affected by an Ulva prolifera Green Tide

Han M, Sun J, Yang Q, Liang Y, Jiang Y, Gao C, et al.

mSystems, 2023 Feb 23.
PMID: 36815859 DOI: 10.1128/msystems.01211-22

The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide. IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.
Nanoplastics potentiate mercury toxicity in a marine copepod under multigenerational exposure

Xie D, Zhang H, Wei H, Lin L, Wang D, Wang M

Aquat Toxicol, 2023 May;258:106497.
PMID: 36940520 DOI: 10.1016/j.aquatox.2023.106497

The continuous fragmentation of plastics and release of synthetic nanoplastics from products have been aggravating nanoplastic pollution in the marine ecosystem. The carrier role of nanoplastics may increase the bioavailability and toxicity effects of toxic metals, e.g., mercury (Hg), which is of growing concern. Here, the copepod Tigriopus japonicus was exposed to polystyrene nanoplastics (PS NPs) and Hg (alone or combined) at environmental realistic concentrations for three generations (F0-F2). Then, Hg accumulation, physiological endpoints, and transcriptome were analyzed. The results showed that the copepod's reproduction was significantly inhibited under PS NPs or Hg exposure. The presence of PS NPs caused significantly higher Hg accumulation, lower survival, and lower offspring production in copepods relative to Hg exposure, suggesting an increased threat to the copepod's survivorship and health. From the molecular perspective, combined PS NPs and Hg caused a graver effect on the DNA replication, cell cycle, and reproduction pathways relative to Hg exposure, linking to lower levels of survivorship and reproduction. Taken together, this study provides an early warning of nanoplastic pollution for the marine ecosystem not only because of their adverse effect per se but also their carrier role for increasing Hg bioaccumulation and toxicity in copepods.
Fulltext Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus

Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, et al.

Virus Res, 2023 Oct 15;336:199226.
PMID: 37739268 DOI: 10.1016/j.virusres.2023.199226

Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.
Fulltext Identification of hidden N4-like viruses and their interactions with hosts

Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, et al.

mSystems, 2023 Sep 13;8(5):e0019723.
PMID: 37702511 DOI: 10.1128/msystems.00197-23

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. IMPORTANCE The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.
Fulltext Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae, Representing a Novel Viral Genus

Guo R, Zheng K, Luo L, Liu Y, Shao H, Guo C, et al.

Microbiol Spectr, 2022 Aug 31;10(4):e0058522.
PMID: 35862991 DOI: 10.1128/spectrum.00585-22

Vibrio parahaemolyticus, a widespread marine bacterium, is responsible for a variety of diseases in marine organisms. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is also known to cause acute gastroenteritis in humans. While numerous dsDNA vibriophages have been isolated so far, there have been few studies of vibriophages belonging to the ssDNA Microviridae family. In this study, a novel ssDNA phage, vB_VpaM_PG19 infecting V. parahaemolyticus, with a 5,572 bp ssDNA genome with a G+C content of 41.31% and encoded eight open reading frames, was isolated. Genome-wide phylogenetic analysis of the total phage isolates in the GenBank database revealed that vB_VpaM_PG19 was only related to the recently deposited vibriophage vB_VpP_WS1. The genome-wide average nucleotide homology of the two phages was 89.67%. The phylogenetic tree and network analysis showed that vB_VpaM_PG19 was different from other members of the Microviridae family and might represent a novel viral genus, together with vibriophage vB_VpP_WS1, named Vimicrovirus. One-step growth curves showed that vB_VpaM_PG19 has a short incubation period, suggesting its potential as an antimicrobial agent for pathogenic V. parahaemolyticus. IMPORTANCE Vibriophage vB_VpaM_PG19 was distant from other isolated microviruses in the phylogenetic tree and network analysis and represents a novel microviral genus, named Vimicrovirus. Our report describes the genomic and phylogenetic features of vB_VpaM_PG19 and provides a potential antimicrobial candidate for pathogenic V. parahaemolyticus.

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