bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphodynamics of non-canonical autophagic structures in
Neurospora crassa
Authors: Rivetta Alberto , Allen Kenneth , Graham Morven , Potapova Tatiana , Slayman Clifford , Liu Xinran 
Published: October 2023

ABSTRACT

Autophagy is a major pathway for unspooling cytoplasmic constituents and recycling them. Here, we investigate autophagy in
Neurospora crassa,
a close ascomycete relative to the model yeast
Saccharomyces cerevisiae
. High-pressure-freeze and freeze-substitution techniques proved keys to preservation of the surprising autophagic structures observed in
Neurospora
by transmission electron microscopy and electron tomography. Depriving
Neurospora
of carbon triggers two parallel processes at the plasma membrane: formation of vacuoles, initially along the plasma membrane but stuffing 70%–80% of cytoplasmic volume after several hours. The vacuoles contain material left over from digested proteins, disrupted ribosomes or glycogen clumps, plus other discrete organelle-like objects. Also, they accumulate the canonical autophagy marker Atg8, appear to be lytic from the start, and probably grow from lysosomes. Formation of diverse phagophores and autophagosomes,
multi-membrane
organelles manufactured
de novo
by the plasma membrane—a feature so far unique to
Neurospora
. These autophagic structures can be observed attached either to the cell membrane, to the cell wall, or free in the cytoplasm, viz. as mature organelles after detachment from the cell membrane. Although phagophores are clearly observed in carbon-replete cells, their production increases with carbon starvation—and these, too, often appear lytic.
ATG1
, the canonical initiator of phagophore formation in yeast, is not required for the formation of phagophores in
Neurospora
. This work provides clear structural and functional evidence that
Neurospora
’s autophagic organelles differ from those observed by others in yeast.

IMPORTANCE

Neurospora
is a quintessential tip-growing organism, which is well known for packaging and longitudinal transport of tip-building blocks. Thus far, however, little attention has been paid to the co-essential process of reclamation, that is—taking apart of upstream, older structural elements, otherwise known as “autophagy”. We are not yet prepared to set out the chemistry of that elaborate process, but its morphological start alone is worthy of attention. Carbon starvation triggers significant autophagic changes, beginning with prolific vacuolation along the plasma membrane, and eventual filling of 70% (or more) of cytoplasmic volume. Additionally, the
Neurospora
plasma membrane elaborates a variety of phagophores which themselves often look lytic. These have either dual enclosing membranes, like the familiar autophagosomes, can be doubled and have four wrapping membranes, or can be compounded with multiple membrane layers. These reclamation processes must be accommodated by the mechanism of tip growth.
Prevalence and genetic characterization of
Campylobacter
from clinical poultry cases in China
Authors: Li Xiaofei , Xu Xiangxiang , Chen Xinyi , Li Yunlu , Guo Jiale , Gao Jie , Jiao Xinan , Tang Yuanyue , Huang Jinlin 
Published: October 2023

ABSTRACT

Campylobacter
is one of the leading causes of bacterial foodborne diseases globally. Poultry is considered a major reservoir for the transmission of
Campylobacter
to humans. The occurrence and epidemiology of
Campylobacter
in healthy poultry have been extensively studied, but the prevalence in diseased poultry has rarely been reported. In this study, a total of 1,563 intestinal samples, 547 gallbladder samples, and 3,729 parenchyma organ samples were collected from diseased chickens, ducks, and geese in Yangzhou Veterinary Hospital between December 2016 and September 2017. The bacterial isolates were analyzed for genotype, resistance, and virulence genes. The overall prevalence of
Campylobacter
was 17.9%, and a significantly higher prevalence was observed in the diseased chickens (21.8%) than in the diseased ducks (12.1%) and geese (11.9%).
Campylobacter
was significantly more prevalent in the intestinal tract (39.6%), followed by the gallbladder (11.7%) and parenchyma organ (9.7%). Among 84 whole-genome sequenced
Campylobacter
isolates, we identified 47 multi-locus sequence typing types, of which ST-51 and ST-825 were the most predominant sequence types (STs) for
Campylobacter jejuni
and
Campylobacter coli
, respectively. Phylogenetic analysis showed that
Campylobacter
isolates from different tissues from the same host tended to cluster together with the same STs, which indicated
Campylobacter
infection in different tissues
in vivo
. The antimicrobial resistance genes most frequently identified were
gyrA
(T86I) (97.6%) and
tet (O)
(65.5%). Our results revealed the high prevalence of
Campylobacter
in diseased poultry in China, which will help the farms take the necessary action to develop effective mitigation strategies for reducing
Campylobacter
infection in poultry.

IMPORTANCE

Campylobacter
is a major cause of campylobacteriosis worldwide, and poultry is the main reservoir for its transmission.
Campylobacter
was generally considered to be a harmless commensal organism in poultry without pathogenic properties. However, it was proposed that a
Campylobacter
-like organism may be the cause of vibrionic hepatitis, which poses a significant public health risk. The occurrence and epidemiology of
Campylobacter
in healthy poultry have been studied systematically, but little is known about the epidemiology of
Campylobacter
isolates from diseased poultry in China. Therefore, this study determined the prevalence and molecular characterization of
Campylobacter
from diseased chickens, ducks, and geese in Yangzhou Veterinary Hospital between December 2016 and September 2017, which was critical for improving the diagnosis and prevention of
Campylobacter
infections.
Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation
Authors: Jiang Hubiao , Luo Jinyan , Liu Quanhong , Ogunyemi Solabomi Olaitan , Ahmed Temoor , Li Bing , Yu Shanhong , Wang Xiao , Yan Chenqi , Chen Jianping , Li Bin 
Published: October 2023

ABSTRACT

Rice bacterial leaf blight (BLB) is the most destructive phyllosphere bacterial disease caused by
Xanthomonas oryzae
pv.
oryzae
. The effect of soil-borne diseases on the rhizosphere microbiome has been extensively investigated. However, the regulatory role of the phyllosphere disease BLB on the rhizosphere microbiome remains unclear. Here, we observed that BLB significantly altered the composition of the bacterial-fungal community in the rhizosphere, decreasing bacterial diversity but not fungal diversity. The scale of inter-kingdom networks in the rhizosphere microbiome of BLB-infected plants was more complex and broader than in healthy plants, while the bacterial community was more vulnerable to BLB than the fungal community. Indeed, the relative abundance of
Streptomyces
,
Chitinophaga
,
Sphingomonas
, and
Bacillus
was higher in the BLB rhizosphere, which can be explained by their keystone hub taxa status in the rhizosphere co-occurrence network. Null model analysis showed that the deterministic assembly of bacterial communities increased while that of fungi decreased. Additionally, the assembly of bacterial and fungal communities was significantly related to variations in BLB and soil nutrients, especially pH and available phosphorus. Random forest model results showed that the bacterial community in the rhizosphere had a strong potential for predicting BLB. Metagenomic analysis revealed that BLB had a considerable impact on the functional adaptation of the rhizosphere microbiome. Interestingly, the abundance of some functional genes involved in carbon, phosphorus, and methane metabolism increased drastically.

IMPORTANCE

Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera
Streptomyces
,
Chitinophaga
,
Sphingomonas
, and
Bacillus
increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.
Community structure and niche differentiation of endosphere bacterial microbiome in
Camellia oleifera
Authors: Zhang Yan , Ding Chu Ting , Jiang Taoya , Liu Yu Hua , Wu Yang , Zhou Hui Wen , Zhang Li Sha , Chen Ye 
Published: October 2023

ABSTRACT

Understanding the changes in bacterial community structure in different microenvironments of
Camellia oleifera
is essential to better explore the benign interaction between beneficial microorganisms and plants. Using
Camellia oleifera
trees, a Chinese wooden oil plant as a model ecosystem, we characterized the archaeal and bacterial microbiome across five different tissue-level niches using 16S rRNA gene analyses. Our research indicates that the diversity of
Camellia oleifera
endophytic bacterial communities is highly dependent on the plant compartment. The species replacement process (69.90%) is the dominant factor in the differences in bacterial community structure. The dominant bacteria phyla (
Proteobacteria
,
Acidobacteria
,
Actinobacteria
,
Bacteroidetes
,
Firmicutes
,
Chloroflexi
, and
Verrucomicrobia
) of
Camellia oleifera
show a significant plant compartment (roots, stems, leaves, fruits) enrichment effects. A variety of bacteria (
Hymenobacter
,
Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium
,
Mesorhizobium
,
Bradyrhizobium
,
Bacillus
,
Ochrobactrum
,
Pantoea
,
Pseudomonas
, etc.) with nitrogen-fixed potentials are enriched in
Camellia oleifera
tissue. In addition, the hub bacterial groups of
Camellia oleifera
are
Nitrospira
,
Haemophilus
,
Staphylococcus
,
Ruminiclostridium
, and
Ochrobactrum
. They are widespread colonization in various tissues with a low relative abundance and may play an important role in the nitrogen cycle, host life promotion, and plant defense. This study provides a holistic understanding of the endosphere bacterial community structure, which is one of the most complete ecological niche-level analyses of
Camellia oleifera
. These results provide a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.

IMPORTANCE

Microorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of
Camellia oleifera
endophytic bacterial communities is highly dependent on the plant compartment.
Proteobacteria
,
Acidobacteria
,
Actinobacteria
,
Bacteroidetes
,
Firmicutes
,
Chloroflexi
, and
Verrucomicrobia
are dominant bacteria phyla. The tissues of
Camellia oleifera
contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.
Maternal transmission of bacterial microbiota during embryonic development in a viviparous lizard
Authors: Montoya-Ciriaco Nina , Hereira-Pacheco Stephanie , Estrada-Torres Arturo , Dendooven Luc , Méndez de la Cruz Fausto R. , Gómez-Acata Elizabeth Selene , Díaz de la Vega-Pérez Aníbal H. , Navarro-Noya Yendi E. 
Published: October 2023

ABSTRACT

The maternal transmission of microbiota during embryonic development of vertebrates is still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA bacterial genes to determine the bacterial communities in the gastrointestinal tract and amniotic environment, i.e., the amniotic fluid, amniotic membrane and extraembryonic yolk, of embryos at the last stage of development of the viviparous lizard
Sceloporus grammicus
Wiegmann, 1828. We compared these communities to those found in the maternal intestine, mouth, cloaca, and the aseptic ventral skin as a control of the aseptic technique. Our results showed that bacterial 16S rRNA genes were present in the embryos of
S. grammicus
. Their diversity was lower and more similar in composition between individuals than those found in the maternal tissues. This suggests that a strong control exists on the transmission of bacteria from the mother to the embryos. We found 78% of the embryonic amplicon sequence variants (ASVs) in the maternal bacterial microbiota, suggesting that the transmission of bacteria from the mother to the embryos is a continuous process and some bacteria may have been transferred during early embryonic stages. The embryonic bacteria were found to overlap mostly with those found in the mouth and aseptic ventral skin of the mother, although it is difficult to conclude that the shared ASVs originated from these maternal tissues. Our study provides evidence of microbiota vertical transfer during embryonic development in the animal kingdom. It also highlights that this maternal transmission could be included in the maternal effects that impact the offspring.

IMPORTANCE

We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard
Sceloporus grammicus
and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues. Most of the bacterial species detected in the embryos were also found in the mother, although not all of them. Interestingly, we detected a high similarity in the composition of bacterial species among embryos from different mothers. These findings suggest that there may be a mechanism controlling the transmission of bacteria from the mother to the embryo. Our results highlight the possibility that the interaction between maternal bacteria and the embryo may affect the development of the lizards.
The formation of lithium-rich pegmatites through multi-stage melting
Authors: Koopmans Lot , Martins Tania , Linnen Robert , Gardiner Nicholas J. , Breasley Catriona M. , Palin Richard M. , Groat Lee A. , Silva David , Robb Laurence J. 
Published: October 2023

Abstract
Lithium-cesium-tantalum–type pegmatites (the primary source of lithium) crystallize from highly evolved, volatile felsic melts that incorporated crustal material in their source. Pegmatites are classically thought to form either from extreme fractionation of a parental granite body or via low-degree partial melting of a metamorphic rock (anatectic origin). However, the processes that lead to the formation of economic lithium pegmatite deposits remain enigmatic, because precipitation of lithium ore minerals requires melt lithium concentrations in excess of 5000 ppm—~500 times upper crustal abundances. We use petrological modeling to quantify lithium enrichment in an anatectic-origin scenario and show that it is primarily driven by the relative stability of residual biotite and muscovite at medium to high pressures (~8 kbar), and biotite and cordierite at low pressures (~3 kbar). We show anatexis of an average lithium-enriched metasedimentary source cannot sufficiently elevate the lithium content of the ensuing melt to form economic deposits; however, if this first-generation melt—now crystallized as granitic crust—is re-melted, the second-generation melt will be sufficiently concentrated in lithium to crystallize lithium ore minerals. We propose a petrogenetic model for anatectic-origin lithium pegmatites, in which a region experiences at least two stages of partial melting, ultimately generating lithium-rich melts without invoking extensive fractional crystallization. This mechanism can both account for the occurrence of unzoned lithium pegmatites and explain why economic pegmatites in many terranes are younger than their inferred source granites.
Characterisation of a novel missense mutation in theERCC5gene leading to group G xeroderma pigmentosum/Cockayne syndrome overlap
Authors: Stehnach William Christopher , Cantor Aaron , Bongiorno Michelle 
Published: October 2023

Xeroderma pigmentosum–Cockayne syndrome complex (XP–CS) is exceedingly rare, with 43 cases described over the past five decades; 21 of these cases exhibited mutations in the ERCC5 endonuclease associated with xeroderma pigmentosum, group G.We report the first known phenotypic characterisation of the homozygous chromosome 13ERCC5, Exon 11, c.2413G>A (p.Gly805Arg) missense mutation in a female toddler presenting with findings of both XP and CS.Her severe presentation also questions previous hypotheses that only truncating mutations and early missense mutations of XPG are capable of producing the dire findings of XP–CS.
Circumstances that promote social connectedness in older adults participating in intergenerational programmes with adolescents: a realist review
Authors: Simionato Jessica , Vally Hassan , Archibald Daryll 
Published: October 2023

ObjectivesLimited social connectedness in older adults is a risk factor for poor physical and mental health. Older adults who are socially isolated, lonely and disconnected have a higher risk of chronic illness, depression and premature death. Current literature suggests that improved social connectedness reduces these risks. Intergenerational programmes are an effective way to improve health outcomes. Despite this, there is yet to be a review using realist review methods that seeks to identify the circumstances that promote social connectedness in older adults participating in intergenerational programmes with adolescents.DesignA realist review methodology was chosen to account for the complexity of intergenerational interventions. Nine studies were included. In line with realist review methodology, iterative data extraction and analysis was conducted to identify the specific contexts, mechanisms and outcomes of the programmes. Specific circumstances were identified to develop theories relating to improved social connectedness in older adults.Data sourcesMEDLINE, PsycINFO, CINAHL were searched using English language limitation.Eligibility criteriaIncluded participants were aged 65 and over (older adults) and between 13 and 19 years (adolescents) participating in intergenerational programmes from non-familial generations. Studies had to be published in English between 2000 and 2020 and could be quantitative, qualitative or mixed-methods primary research studies.Data extraction and synthesisTwo independent reviewers used a bespoke data extraction form. All authors were involved in the synthesis process which used the extracted data to illuminate the contexts, mechanisms and outcomes that underpinned reviewed programmes.ResultsThe nine included studies were set in different contexts, including community organisations, schools and aged care facilities. They used an array of interventions including reminiscence therapy, craft or space for conversation. Despite study heterogeneity, the parallels in psychosocial development between older adults and adolescents were shown to be a likely driver for improved social health outcomes. Programmes most likely to improve social health outcomes were those that acknowledged psychosocial development, were delivered in community settings, leveraged pedagogical frameworks, used trained facilitators and supported participants to build relationships through shared purpose.ConclusionsThis review contributes a logic model to support the design and development of intergenerational programmes involving adolescents to improve social connectedness in older adults. Future research to test the logic model in practice is needed.
Exploring the postoperative pain experiences of individuals with opioid use disorder and the nurses providing care in the USA: A qualitative descriptive study protocol
Authors: Pavone Kara , Gorgol Hilary , Rust Victoria , Bronski Mary , Labelle Colleen , Compton Peggy 
Published: October 2023

IntroductionThe goal of this study is to gain firsthand insights from individuals with a history of opioid use disorder (OUD) using medication for OUD on their experiences with postoperative pain care. This study also seeks to describe the experiences of nurses caring for individuals with OUD, and the challenges they may face managing complaints of pain in this population. Research suggests that hospitals can significantly enhance the quality of the care they deliver by investigating an individual’s experience in the care setting. These insights will allow for the development of strategies for nurses to deepen their understanding of and, therefore, advocate and improve care for, this vulnerable and often stigmatised population.Methods and analysisA qualitative descriptive study will be conducted consisting of a prescreening and demographics questionnaire, and individual semistructured interviews with approximately 10–15 individuals with OUD having recently undergone surgery and 10–15 nurses providing care for this population for a total of 20–30 interviews. This approach involves the collection of separate but complementary data (ie, perceptions of individuals with OUD and nurses) concerning the phenomena of postoperative pain management. Sampling will continue until data saturation is reached. Descriptive statistics and thematic analysis will then be used. Reporting will adhere to the Standards for Reporting Qualitative Research checklist.Ethics and disseminationThis study received approval from the Institutional Review Board at Northeastern University. Alongside peer-reviewed journal publications, the findings will be presented at relevant conferences, and a plain language summary will be distributed to the study participants.