bluuebunny/crossref_metadata_2025 huggingface dataset:
Ability of Adjusting Grip Strength From Childhood to Adulthood
Authors: Ohtaka Chiaki , Fujiwara Motoko
Published: December 2023

Purpose: This cross-sectional study aimed to investigate the ability to adjust grip strength by comparing the characteristics of force generation and relaxation from childhood to adulthood. Method: This study included 225 participants aged 6, 11, 17, and 19–23 years (adults) who performed isometric hand-grip force as follows: maximum, half generation, and half relaxation. The force was recorded, and relative values and errors were calculated for half tasks. Results: The maximum task values increased with age, but there was no significant age difference between 17-year-olds and adults. The difference between sexes was significant; males were stronger than females in both 17-year-olds and adults. Both sexes in all age groups had greater errors in half relaxation than in half generation tasks. Females had negatively greater constant error than males in half tasks. The errors of 6-year-olds were greater than the other age groups in half tasks. Conclusion: There is a developmental trend for producing maximal strength that is similar across sexes until adolescence when males are stronger and females plateau. The ability of force relaxation was more difficult to accurately control than force generation for all age groups and was adult-like by middle childhood.
Does Knowledge of Results Affect Motor Skill Learning and Adaptation in Interception-Like Tasks?
Authors: Leite Cláudio Manoel Ferreira , Ugrinowitsch Herbert , Couto Crislaine Rangel
Published: December 2023

Knowledge of results (KR), particularly its informational role, has often been regarded as redundant for learning interception-like tasks, such as coincidence–anticipation timing tasks. However, it is possible that the KR’s guiding effect might be detrimental to motor adaptation, instead of only redundant, leading to a dependency on KR and steering the sensorimotor system away from relevant information of the task. In this study, we aimed to investigate KR’s effect on learning a coincidence–anticipation timing tasks and on the adaptation to unpredictable perturbations. Two groups of participants practiced a coincidence–anticipation timing tasks with or without KR on 1 day and underwent testing the next day for learning (Retention test) and for adaptation to unpredictable perturbations (Exposure phase). Both groups exhibited similar learning results but failed to adapt to the perturbations, contradicting the assumption of negative guidance effects of KR and the positive effects of relying solely on intrinsic information (no KR). These findings suggest that motor adaptation may require specific information during the acquisition process, highlighting for more systematic analyses to understand this phenomenon better. Such insights could have practical implications in contexts like sports and rehabilitation, by providing learners with appropriate information for acquiring adaptive internal representations of tasks.
A Systematic Review of Physical Activity and Sedentary Behavior Patterns in an Osteoarthritic Population
Authors: Dawson Zoe E. , Beaumont Alexander J. , Carter Sophie E.
Published: December 2023

Objective: To explore physical activity (PA) and sedentary behaviors (SB) in individuals with lower limb (LL) Osteoarthritis (OA) and the influence of age, sex, and body mass index (BMI) on these behaviors. Design: Systematic review search: PubMed, Cochrane Library, ScienceDirect, and CINAHL databases were searched from inception until July 2023. Study criteria: Studies that reported quantifiable device-based or self-reported data for PA and SB variables in adults clinically diagnosed with LL OA were included. Data synthesis: A synthesis of PA and SB levels for those diagnosed with LL OA and the influence age, sex, and BMI have on these behaviors. Results: From the 1930 studies identified through the electronic search process, 48 met the inclusion criteria. PA guidelines were met by 33% of the sample population that measured moderate and moderate to vigorous PA. No studies reported 75 minutes per week or more of vigorous PA. Additionally, 58% of the population reporting SB were sedentary for 8 hours per day or more. Also, increasing age, BMI, and the female sex were identified as negative influences on PA levels. There were numerous methodological inconsistencies in how data were collected and reported, such as various activity monitor cut points for PA and SB bout duration. Conclusion: Adults with LL OA may be at an increased risk of noncommunicable diseases due to low PA and high SB levels. It is important to consider age, sex, and BMI when investigating behavior patterns in those with LL OA.
Divergent genetic landscapes drive lower levels of AmpC induction and stable de-repression in
Serratia marcescens
compared to
Enterobacter cloacae
Authors: Lazarus Jacob E. , Wang Yin , Waldor Matthew K. , Hooper David C.
Published: December 2023

The chromosomally encoded AmpC beta-lactamase is widely distributed throughout the Enterobacterales. When expressed at high levels through transient induction or stable de-repression, resistance to ceftriaxone, a commonly used antibiotic, can develop. Recent clinical guidance suggests, based on limited evidence, that resistance may be less likely to develop in
Serratia marcescens
compared to the better-studied
Enterobacter cloacae
and recommends that ceftriaxone may be used if the clinical isolate tests susceptible. We sought to generate additional data relevant to this recommendation. AmpC de-repression occurs predominantly because of mutation in the
ampD
peptidoglycan amidohydrolase. We find that, in contrast to
E. cloacae
, where deletion of
ampD
results in high-level ceftriaxone resistance (with ceftriaxone MIC = 96 µg/mL), in
S. marcescens
deletion of two amidohydrolases (
ampD
and
amiD2
) is necessary for AmpC de-repression, and the resulting ceftriaxone MIC is 1 µg/mL. Two mechanisms for this difference were identified. We find both a higher relative increase in
ampC
transcript level in
E. cloacae
Δ
ampD
compared to
S. marcescens ΔampDΔamiD2
, as well as higher
in vivo
efficiency of ceftriaxone hydrolysis by the
E. cloacae
AmpC enzyme compared to the
S. marcescens
AmpC enzyme. We also observed higher relative levels of transient AmpC induction in
E. cloacae
vs
S. marcescens
when exposed to ceftriaxone. In time-kill curves, this difference translates into the survival of
E. cloacae
but not
S. marcescens
at clinically relevant ceftriaxone concentrations. In summary, our findings can explain the decreased propensity for on-treatment ceftriaxone resistance development in
S. marcescens
, thereby supporting recently issued clinical guidance.
Genetic and enzymatic characterization of Amy13E from
Cellvibrio japonicus
reclassifies it as a cyclodextrinase also capable of α-diglucoside degradation
Authors: Mascelli Giulia M. , Garcia Cecelia A. , Gardner Jeffrey G.
Published: December 2023

Cyclodextrinases are carbohydrate-active enzymes involved in the linearization of circular amylose oligosaccharides. Primarily thought to function as part of starch metabolism, there have been previous reports of bacterial cyclodextrinases also having additional enzymatic activities on linear malto-oligosaccharides. This substrate class also includes environmentally rare α-diglucosides such as kojibiose (α−1,2), nigerose (α−1,3), and isomaltose (α−1,6), all of which have valuable properties as prebiotics or low-glycemic index sweeteners. Previous genome sequencing of three
Cellvibrio japonicus
strains adapted to utilize these α-diglucosides identified multiple, but uncharacterized, mutations in each strain. One of the mutations identified was in the
amy13E
gene, which was annotated to encode a neopullulanase. In this report, we functionally characterized this gene and determined that it in fact encodes a cyclodextrinase with additional activities on α-diglucosides. Deletion analysis of
amy13E
found that this gene was essential for kojibiose and isomaltose metabolism in
C. japonicus
. Interestingly, a Δ
amy13E
mutant was not deficient for cyclodextrin or pullulan utilization in
C. japonicus
; however, heterologous expression of the gene in
E. coli
was sufficient for cyclodextrin-dependent growth. Biochemical analyses found that
Cj
Amy13E cleaved multiple substrates but preferred cyclodextrins and maltose, but had no activity on pullulan. Our characterization of the
Cj
Amy13E cyclodextrinase is useful for refining functional enzyme predictions in related bacteria and for engineering enzymes for biotechnology or biomedical applications.

IMPORTANCE

Understanding the bacterial metabolism of cyclodextrins and rare α-diglucosides is increasingly important, as these sugars are becoming prevalent in the foods, supplements, and medicines humans consume that subsequently feed the human gut microbiome. Our analysis of a cyclomaltodextrinase with an expanded substrate range is significant because it broadens the potential applications of the GH13 family of carbohydrate active enzymes (CAZymes) in biotechnology and biomedicine. Specifically, this study provides a workflow for the discovery and characterization of novel activities in bacteria that possess a high number of CAZymes that otherwise would be missed due to complications with functional redundancy. Furthermore, this study provides a model from which predictions can be made why certain bacteria in crowded niches are able to robustly utilize rare carbon sources, possibly to gain a competitive growth advantage.
Maximizing the
Neisseria gonorrhoeae
confirmatory rate and the genotypic detection of ciprofloxacin resistance for samples screened with cobas CT/NG
Authors: Pryce Todd M. , Foti Olivia R. , Haygarth Erin J. , Whiley David M.
Published: December 2023

Supplementary nucleic acid amplification testing for
Neisseria gonorrhoeae
(NG) is widely used to circumvent specificity problems associated with extragenital sites. Here, we compared different supplementary approaches for confirming NG-positive samples from the cobas 4800 CT/NG (c4800) and cobas 6800 CT/NG (c6800) assays using the
ResistancePlus
GC (RP-GC) assay, which in addition to detecting NG, also predicts ciprofloxacin susceptibility via NG
gyrA
characterization. Two different nucleic acid extraction techniques were investigated for RP-GC detection; extracts from c4800 (c4800-RP-GC) and MagNA Pure 96 (MP96-RP-GC). NG-positive (
n
= 300) and -negative (
n
= 150) samples in cobas PCR media from routine c4800 testing were retrospectively retested with c4800, c6800, c4800-RP-GC, and MP96-RP-GC. Selected samples were also tested with Xpert CT/NG (Xpert) for discrepant analysis. The
gyrA
status was compared to ETEST ciprofloxacin susceptibility or non-susceptibility for recovered isolates (
n
= 63). Extragenital confirmatory rates were higher for MP96-RP-GC (131/140; 93.6%) compared to c4800-RP-GC (126/146; 86.3%), albeit not significantly (
P
= 0.6677). Of 9 samples testing positive by c6800 and negative by MP96-RP-GC, 7/9 (77.8%) were also negative by Xpert. By contrast, the number of samples returning a valid
gyrA
status was significantly (
P
= 0.0003) higher for MP96-RP-GC (270/293; 92.2%) compared to c4800-RP-GC (245/298; 82.2%). The overall MP96-RP-GC
gyrA
status correlated 98.4% (61/62) with the reported ciprofloxacin sensitive (35/36; 97.2%) or non-susceptible (26/26; 100%) phenotype. Improved RP-GC confirmatory rates and reported
gyrA
status were observed using MP96 nucleic acids compared to c4800 extracts. The data further highlight the ongoing need for NG supplemental testing for oropharyngeal samples.
A nanobody inhibiting porcine reproductive and respiratory syndrome virus replication via blocking self-interaction of viral nucleocapsid protein
Authors: Duan Hong , Chen Xu , Zhang Ziwei , Zhang Zhijie , Li Zhihan , Wang Xinjie , Zhao Jiakai , Nan Yuchen , Liu Baoyuan , Zhang Angke , Sun Yani , Zhao Qin
Published: December 2023

Porcine reproductive and respiratory syndrome (PRRS) is a serious global pig industry disease. Understanding the mechanism of viral replication and developing efficient antiviral strategies are necessary for combating with PRRS virus (PRRSV) infection. Recently, nanobody is considered to be a promising antiviral drug, especially for respiratory viruses. The present study evaluated two nanobodies against PRRSV nucleocapsid (N) protein (PRRSV-N-Nb1 and -Nb2) for their anti-PRRSV activity
in vitro
and
in vivo
. The results showed that intracellularly expressed PRRSV-N-Nb1 significantly inhibited PRRSV-2 replication in MARC-145 cells (approximately 100%). Then, the PRRSV-N-Nb1 fused with porcine IgG Fc (Nb1-pFc) as a delivering tag was produced and used to determine its effect on PRRSV-2 replication in porcine alveolar macrophages (PAMs) and pigs. The inhibition rate of Nb1-pFc against PRRSV-2 in PAMs could reach >90%, and it can also inhibit viral replication
in vivo
. Epitope mapping showed that the motif Serine 105 (S105) in PRRSV-2 N protein was the key amino acid binding to PRRSV-N-Nb1, which is also pivotal for the self-interaction of N protein via binding to Arginine 97. Moreover, viral particles were not successfully rescued when the S105 motif was mutated to Alanine (S105A). Attachment, entry, genome replication, release, docking model analysis, and blocking enzyme-linked immunosorbent assay (ELISA) indicated that the binding of PRRSV-N-Nb1 to N protein could block its self-binding, which prevents the viral replication of PRRSV. PRRSV-N-Nb1 may be a promising drug to counter PRRSV-2 infection. We also provided some new insights into the molecular basis of PRRSV N protein self-binding and assembly of viral particles.

IMPORTANCE

Porcine reproductive and respiratory syndrome virus (PRRSV) causes serious economic losses to the swine industry worldwide, and there are no highly effective strategies for prevention. Nanobodies are considered a promising novel approach for treating diseases because of their ease of production and low costing. Here, we showed that PRRSV-N-Nb1 against PRRSV-N protein significantly inhibited PRRSV-2 replication
in vitro
and
in vivo
. Furthermore, we demonstrated that the motif Serine 105 (S105) in PRRSV-N protein was the key amino acid to interact with PRRSV-N-Nb1 and bond to its motif R97, which is important for the self-binding of N protein. The PRRSV-N-Nb1 could block the self-interaction of N protein following viral assembly. These findings not only provide insights into the molecular basis of PRRSV N protein self-binding as a key factor for viral replication for the first time but also highlight a novel target for the development of anti-PRRSV replication drugs.
Hepatitis C virus modified sE2
F442NYT
as an antigen in candidate vaccine facilitates human immune cell activation
Authors: Haga Yuki , Meyer Keith , Sung Molly M. H. , Reagan Erin K. , Weissman Drew , Ray Ranjit
Published: December 2023

The rational selection of hepatitis C virus (HCV) vaccine antigen will aid in the prevention of future chronic liver disease burden and associated healthcare costs. We have previously shown that HCV E2 glycoprotein is not highly immunogenic, and the modification of E2 reduced CD81 binding and displayed altered cytokine and protective immune responses
in vitro
and in a surrogate mouse model. Here, we compared the influence of a parental and a modified sE2
F442NYT
glycoprotein region from HCV genotype 1a for the activation of peripheral blood mononuclear cell (PBMC)-derived dendritic cells (DCs), CD4
+
T cells, and B cells. Modified sE2
F442NYT
, when incubated with DCs, induced a higher number of CD86-positive cells. The sE2
F442NYT
or parental sE2 encapsulated as mRNA-lipid nanoparticle (sE2
F442NYT
mRNA-LNP) primed DCs co-cultured with autologous CD4
+
T cells did not induce CD25 or forkhead box P3 expression. PBMC-derived CD4
+
T cells treated with sE2
F442NYT
exhibited enhanced signal transducer and activator of transcription (Stat)1/Stat4 phosphorylation in response to anti-CD3/CD28 stimulation in comparison to parental sE2 treatment and facilitated isotype switching in B cells, leading to the generation of a broader subclass of antibodies. Cells treated with modified sE2
F442NYT
displayed an increase in activated Stat3 and extracellular signal-regulated kinase (ERK). Likewise, PBMC-derived naïve B cells upon
in vitro
stimulation with sE2
F442NYT
induced an increased proliferation, Stat3 and ERK activation, and protein kinase B (Akt) suppression. Thus, the modified sE2
F442NYT
antigen from HCV facilitates improved DC, CD4
+
T, and B cell activation compared to parental sE2 to better induce a robust protective immune response, supporting its selection as an HCV candidate vaccine antigen for preclinical and clinical HCV vaccine trials.

IMPORTANCE

The nature of an enhanced immune response induced by sE2
F442NYT
will help in the selection of a broad cross-protective antigen from hepatitis C virus genotypes, and the inclusion of relatively conserved sE1 with sE2
F442NYT
may further strengthen the efficacy of the candidate vaccine in evaluating it for human use.
Mentoring across difference and distance: building effective virtual research opportunities for underrepresented minority undergraduate students in biological sciences
Authors: Knox Corey J. , Ab Latif Faqryza M. , Cornejo Natasha R. , Johnson Michael D. L.
Published: December 2023

The National Summer Undergraduate Research Program (NSURP) is a mentored summer research program in biosciences for undergraduate students from underrepresented backgrounds in science, technology, engineering, and mathematics (STEM). Conducted virtually over 8 weeks every summer starting in 2020, NSURP provides accessible and flexible research experiences to meet the needs of geographically diverse and schedule-constrained students. Drawing from mentee reporting and surveys conducted within the NSURP framework involving over 350 underrepresented minority undergraduate students over three cohorts (2020–2022), matched with mentors, this paper highlights the potential benefits of students participating in virtual mentored research experiences. In addition to increased access to quality research experiences for students who face travel or academic setting constraints, we found that virtual mentoring fosters cross-cultural collaborations, generates novel research questions, and expands professional networks. Moreover, this study emphasizes the role of virtual mentorship opportunities in fostering inclusivity and support for individuals from underrepresented groups in STEM fields. By overcoming barriers to full participation in the scientific community, virtual mentorship programs can create a more equitable and inclusive environment for aspiring researchers. This research contributes to the growing body of literature on the effectiveness and the potential of virtual research programs and mentorship opportunities in broadening participation and breaking down barriers in STEM education and careers.

IMPORTANCE

Summer Research Experiences for Undergraduates (REUs) are established to provide platforms for interest in scientific research and as tools for eventual matriculation to scientific graduate programs. Unfortunately, the COVID-19 pandemic forced the cancellation of in-person programs for 2020 and 2021, creating the need for alternative programming. The National Summer Undergraduate Research Project (NSURP) was created to provide a virtual option to REUs in microbiology to compensate for the pandemic-initiated loss of research opportunities. Although in-person REUs have since been restored, NSURP currently remains an option for those unable to travel to in-person programs in the first place due to familial, community, and/or monetary obligations. This study examines the effects of the program's first 3 years, documenting the students’ experiences, and suggests future directions and areas of study related to the impact of virtual research experiences on expanding and diversifying science, technology, engineering, and mathematics.
Evidence for Rho-dependent control of a virulence switch in
Acinetobacter baumannii
Authors: Pérez-Varela María , Singh Raja , Colquhoun Jennifer M. , Starich Olivia G. , Tierney Aimee R. P. , Tipton Kyle A. , Rather Philip N.
Published: December 2023

Acinetobacter baumannii
strain AB5075 is able to interconvert at high frequency between virulent cells that form opaque colonies (VIR-O) and avirulent cells that form translucent colonies (AV-T). Cells switch from the VIR-O to the AV-T state by the combinatorial activation of at least three TetR-type transcriptional regulators (TTTRs). A genetic screen identified the transcription termination factor Rho as a major contributor that controls expression differences of these TTTRs between VIR-O and AV-T cells. Each TTTR has a long mRNA leader region where transcripts are terminated in VIR-O cells. However, in AV-T cells, the degree of termination in each TTTR leader was greatly reduced, allowing for higher levels of TTTR expression. In a strain with decreased Rho expression, or in wild-type VIR-O cells treated with the Rho inhibitor bicyclomycin, the degree of termination in each TTTR mRNA leader region was reduced. Mutations in the leader region of one TTTR,
ABUW_1645
, were identified that reduced the degree of termination. Purified Rho protein bound the leader region of the most frequently activated TTTR
ABUW_1645
and the least frequently activated TTTR
ABUW_1959
with similar affinities. This together with the observation that the levels of Rho protein were unchanged between VIR-O and AV-T cells, suggested that additional factors differentially modulate Rho activity between each variant. Finally, we demonstrate in AV-T cells that nutrient depletion is a condition that increases the levels of Rho-dependent transcription termination in the TTTR leader regions to regulate this phenotypic switch.

IMPORTANCE

Acinetobacter baumannii
is a significant cause of infections in the healthcare setting. More recently,
A. baumannii
has been a leading cause of secondary bacterial pneumonia in patients infected with SARS-CoV-2 and the overall frequency of
A. baumannii
infection increased 78% during the COVID-19 pandemic.
A. baumannii
can exist in virulent or avirulent subpopulations and this interconversion is mediated by the expression of a family of TetR-type transcriptional regulators. In this study, we demonstrate that Rho is a key regulatory component in the expression of these TetR regulators. Overall, this study is the first to address a role for Rho in
A. baumannii
and provides additional evidence for the role of Rho in regulating diversity in bacterial subpopulations.
Type IV pilus retraction is required for
Neisseria musculi
colonization and persistence in a natural mouse model of infection
Authors: Rhodes Katherine A. , Rendón María A. , Ma Man Cheong , Agellon Al , Johnson Andrew C.E. , So Magdalene
Published: December 2023

Retraction of the pathogenic
Neisseria
Type IV pilus (Tfp) requires PilT, the primary retraction motor, and its paralogs PilU and PilT2. The importance of Tfp retraction for natural infection is unknown. Using our natural animal model of
Neisseria
-host interaction, we have examined the role of these proteins in the ability of commensal
Neisseria musculi
(Nmus) to colonize and persist in its native host, the mouse. We report that Nmus Δ
pilT
cannot colonize mice; Δ
pilU
and Δ
pilT2
can colonize and persist in mice, but in lower numbers. Microcolonies formed by Δ
pilT
, Δ
pilTU
, and

pilT
L201C

, expressing PilT with a point mutation in its ATP hydrolysis domain, are sensitive to removal by fluid shear forces. Thus, PilT promotes Nmus colonization while PilU and PilT2 influence persistence. We present a non-exclusive model for how these Tfp retraction motor proteins contribute to Nmus persistent colonization. Our findings have implications for the roles of these motor proteins in mediating interactions of human-adapted pathogenic and commensal
Neisseria
with their human host.

IMPORTANCE

We describe the importance of Type IV pilus retraction to colonization and persistence by a mouse commensal
Neisseria, N. musculi,
in its native host. Our findings have implications for the role of Tfp retraction in mediating interactions of human-adapted pathogenic and commensal
Neisseria
with their human host due to the relatedness of these species.
Sua5 catalyzing universal t
6
A tRNA modification is responsible for multifaceted functions of the KEOPS complex in
Cryptococcus neoformans
Authors: Choi Yeseul , Hyeon Hana , Lee Kangseok , Bahn Yong-Sun
Published: December 2023

The N
6
-threonylcarbamoyl adenosine (t
6
A) tRNA modification is critical for ensuring translation fidelity across three domains of life. Our prior work highlighted the KEOPS complex, organized in a Pcc1-Kae1-Bud32-Cgi121 linear arrangement, not only serves an evolutionarily conserved role in t
6
A tRNA modification but also exerts diverse functional impacts on pathobiological characteristics in
Cryptococcus neoformans
, a leading cause of fungal meningitis worldwide. However, the extent to which the pleiotropic functions of the KEOPS complex are specifically tied to tRNA modification remains uncertain. To address this, we undertook a functional characterization of Sua5, responsible for generating the precursor threonylcarbamoyl-adenylate (TC-AMP) for t
6
A tRNA modification, using a reverse genetics approach. Comparative phenotypic analyses with KEOPS mutants revealed that Sua5 plays a vital role in multiple cellular processes, such as t
6
A tRNA modification, growth, sexual development, stress response, and virulence factor production, thus reflecting the multifaceted functions of the KEOPS complex. In support of this,
sua5
Δ
bud32
Δ double mutants showed phenotypes comparable to those of the corresponding single mutants. Intriguingly, a
SUA5
allele lacking a mitochondria targeting sequence (

SUA5
MTS

Δ
) was sufficient to restore the wild-type phenotypes in the
sua5
Δ mutant, suggesting that Sua5’s primary functional locus may be cytosolic, akin to the KEOPS complex. Further supporting this, the deletion of Qri7, a mitochondrial paralog of Kae1, had no discernible phenotypic impact on
C. neoformans
. We concluded that cytosolic t
6
A tRNA modifications, orchestrated by Sua5 and the KEOPS complex, are central to the regulation of diverse pathobiological functions in
C. neoformans
.

IMPORTANCE

Understanding cellular functions at the molecular level is crucial for advancing disease treatments. Our research reveals a critical connection between the KEOPS complex and Sua5 in
Cryptococcus neoformans
, a significant cause of fungal meningitis. While the KEOPS complex is known for its versatile roles in cellular processes, Sua5 is specialized in t
6
A tRNA modification. Our key finding is that the diverse roles of the KEOPS complex, ranging from cell growth and stress response to virulence, are fundamentally linked to its function in t
6
A tRNA modification. This conclusion is supported by the remarkable similarities between the impacts of Sua5 and KEOPS on these processes, despite their roles in different steps of the t
6
A modification pathway. This newfound understanding deepens our insight into fungal biology and opens new avenues for developing potential therapies against dangerous fungal diseases.
Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments
Authors: Yang Luhua , Guo Yuan , Yang Hui , Li Shun , Zhang Yunzeng , Hao Likai
Published: December 2023

The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.

IMPORTANCE

The presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system’s barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.
Mycothione reductase as a potential target in the fight against
Mycobacterium abscessus
infections
Authors: Piller T. , De Vooght L. , Gansemans Y. , Van Nieuwerburgh F. , Cos P.
Published: December 2023

While infections caused by
Mycobacterium abscessus
complex (MABC) are rising worldwide, the current treatment of these infections is far from ideal due to its numerous shortcomings thereby increasing the urge for novel drug targets. In this study, mycothione reductase (Mtr) was evaluated for its potential as a drug target for MABC infections since it is a key enzyme needed in the recycling of mycothiol, the main low-molecular-weight thiol protecting the bacteria against reactive oxygen species and other reactive intermediates. First, a
Mab
∆
mtr
mutant strain was generated, lacking
mtr
expression. Next, the
in vitro
sensitivity of
Mab
∆
mtr
to oxidative stress and antimycobacterial drugs was determined. Finally, we evaluated the intramacrophage survival and the virulence of
Mab
∆
mtr
in
Galleria mellonella
larvae.
Mab
∆
mtr
demonstrated a 39.5-fold reduction in IC90 when exposed to bedaquiline
in vitro
. Furthermore, the
Mab
∆
mtr
mutant showed a decreased ability to proliferate inside macrophages and larvae, suggesting that Mtr plays an important role during MABC infection. Altogether, these findings support the assumption of Mtr being a potential target for antimycobacterial drugs.

IMPORTANCE

Mycobacterium abscessus
complex (MABC) is a group of bacteria causing a serious public health problem worldwide due to its ability to cause progressive disease, its highly resistant profile against various antibiotics, and its lengthy treatment. Therefore, new drugs are needed to alleviate antibiotic resistance and reduce the length of the current treatment. A potential new target for new antibiotics is mycothione reductase (Mtr), an important enzyme belonging to a pathway that protects the bacteria against harmful conditions. Our research created a bacterium deficient of
mtr
by using advanced genetic techniques and demonstrated that
mtr
-deficient bacteria have a decreased ability to multiply during infection. Furthermore, we show evidence that currently used antibiotics combined with
mtr
deficiency can lead to a better treatment of MABC infection. Altogether, our results validate Mtr as a potential new target and suggest that Mtr plays a role during MABC infection.
Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle
Authors: Zhang Tao , Mu Yingyu , Gao Yunlong , Tang Yijun , Mao Shengyong , Liu Jinxin
Published: December 2023

A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals’ gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG,
P
< 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.

IMPORTANCE

The increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals’ performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.
Wetlands harbor lactic acid-driven chain elongators
Authors: Candry Pieter , Flinkstrom Zachary , Henriikka Winkler Mari-Karoliina
Published: December 2023

Wetlands are globally significant carbon storage hotspots. Recent research has suggested that microbially derived metabolites may contribute to soil organic matter formation. Identifying pathways driving the formation of such metabolites is critical to understand the global impact of wetland carbon cycling. Here, we evaluate the presence of chain-elongating organisms converting two to three carbon compounds (i.e., lactic and acetic acid) to medium-chain carboxylic acids (MCCA; i.e., six-carbon caproic acid) in wetland soils. We demonstrate the enrichment of a lactic acid-driven chain-elongating community from wetland soils producing a mixture of butyric and caproic acid. The enriched community was dominated by Clostridiaceae, Ruminococcaceae, and Lachnospiraceae, three families with known chain elongators. Amplicon sequencing identified three Ruminococcaceae and one Clostridiaceae zero-radius OTU (zOTU) that were (i) present in the soil, (ii) enriched over 1% relative abundance in the bioreactor, and (iii) were closely related to known chain elongators. Moreover, close relatives of the three Ruminococcaceae zOTU were also observed in several other wetland microbiomes. From this observation, we conclude that close relatives of known chain elongators, potentially capable of lactic acid-driven MCCA production themselves, are present in wetland soils. This observation may have implications for our understanding of carbon cycling and storage in wetland ecosystems.

IMPORTANCE

Wetlands are globally significant carbon cycling hotspots that both sequester large amounts of CO
2
as soil carbon as well as emit a third of all CH
4
globally. Their outsized role in the global carbon cycle makes it critical to understand microbial processes contributing to carbon breakdown and storage in these ecosystems. Here, we confirm the presence of chain-elongating organisms in freshwater wetland soils. These organisms take small carbon compounds formed during the breakdown of biomass and turn them into larger compounds (six to eight carbon organic acids) that may potentially contribute to the formation of soil organic matter and long-term carbon storage. Moreover, we find that these chain-elongating organisms may be widely distributed in wetlands globally. Future work should identify these organisms’ contribution to carbon cycling in wetlands and the potential role of the products they form in carbon sequestration in wetlands.
Controls on topography and erosion of the north-central Andes
Authors: Leonard Joel S. , Whipple Kelin X. , Heimsath Arjun M.
Published: December 2023

We present 17 new 10Be erosion rates from southern Peru sampled across an extreme orographic rainfall gradient. Using a rainfall-weighted variant of the normalized channel steepness index, ksnQ, we show that channel steepness values, and thus topography, are adjusted to spatially varying rainfall. Rocks with similar physical characteristics define distinct relationships between ksnQ and erosion rate (E), suggesting ksnQ is also resolving lithologic variations in erodibility. However, substantial uncertainty exists in parameters describing these relationships. By combining our new data with 38 published erosion rates from Peru and Bolivia, we collapse the range of compatible parameter values and resolve robust, nonlinear ksnQ–E relationships suggestive of important influences of erosional thresholds, rock properties, sediment characteristics, and temporal runoff variability. In contrast, neither climatic nor lithologic effects are clear using the traditional channel steepness metric, ksn. Our results highlight that accounting for spatial rainfall variations is essential for disentangling the multiple influences of climate, lithology, and tectonics common in mountain landscapes, which is a necessary first step toward greater understanding of how these landscapes evolve.
Wernicke encephalopathy: limitations in a laboratory and radiological diagnosis
Authors: Ono Kohei , Hayano Satoshi , Kashima Masayuki
Published: December 2023

Wernicke encephalopathy is an emergent neurological disorder caused by vitamin B1(thiamine) deficiency. Here, we present a case of Wernicke encephalopathy in a male patient in his 70s with normal serum thiamine levels and MRI findings on admission. He had a history of heavy alcohol consumption and a gradual decrease in food intake. On arrival at the hospital, his consciousness was impaired which persisted even after glucose replacement. Moreover, horizontal nystagmus and cerebellar ataxia were observed. Head CT scan and MRI revealed no abnormal findings. Further, his serum thiamine level was within the normal range. The patient was clinically diagnosed with Wernicke encephalopathy, and high-dose thiamine therapy was started. Then, his symptoms improved immediately. Thus, in case of clinical suspicion, treatment for Wernicke encephalopathy must be initiated promptly even in patients with normal serum thiamine levels.
High-grade dysplasia of the cystic duct margin: how should this be managed?
Authors: Andersen Lalita Maria , Goh Ian Y , Siriwardhane Mehan
Published: December 2023

High-grade dysplasia (HGD) in the cystic duct is a rare epithelial lesion that may lead to biliary tract malignancy. Due to its association with aggressive multifocal cholangiocarcinoma, it is important to investigate for concurrent malignancy, remove all areas of HGD and monitor for recurrence or metastasis.

We present a case of a woman in her 60s with cholecystitis who underwent a laparoscopic cholecystectomy. On histopathology, the patient was found to have incidental HGD involving the cystic duct margin. After ensuring the absence of concurrent malignancy on cross-sectional imaging, she underwent further resection until the margins were clear of dysplasia. In the absence of clear follow-up guidelines, the patient was closely monitored with outpatient scans for up to 5 years.
Anterior hypopituitarism due to primary empty sella syndrome in a critically unwell patient
Authors: Rajesh Mariya , Omer Tahir , Chinniah Sadasivan
Published: December 2023

A previously fit and well male in his early 40s, presented to the emergency department, hypotensive, bradycardic and hypothermic with reduced levels of consciousness after being found diaphoretic and unwell at his home. Despite fluid resuscitation with warmed saline, he remained hypotensive and required vasopressor support leading to intensive care admission. Initially, the patient was managed for suspected meningoencephalitis but was later found to have hypopituitarism leading to secondary hypothyroidism and adrenal insufficiency. Subsequent investigations revealed it is due to empty sella syndrome.
Peripancreatic tuberculosis
Authors: Aggarwal Sunita , Nandi Sudipta , Verma Abhishek , Kumar Naresh
Published: December 2023

Peripancreatic tuberculosis (PTB) is a very rare variant of tuberculosis and its clinical and radiological findings are similar to those of pancreatic malignancy. Diagnosis of PTB is usually incidental and is made after surgical resection. We are presenting a male patient who had complaints of prolonged fever, significant weight loss and yellowish discolouration of eyes and dark-coloured urine. Investigations revealed that there was a pancreatic mass causing obstructive jaundice. However, the aetiology of the mass, whether tubercular or malignant, was not clear. Hence, the patient was planned for endoscopic ultrasound-guided fine needle aspiration cytology. Cytology and aspirate were sent for a cartridge-based nucleic acid amplification test which revealed the presence ofMycobacterium tuberculosis, sensitive to rifampicin. The patient improved completely after treatment with antitubercular therapy.
Uterine rupture of an unscarred gravid uterus at term attributed to adenomyosis
Authors: Phillips Lucy , Brown Heather , Williams Anthony
Published: December 2023

Uterine rupture is a rare obstetric emergency that is typically associated with the presence of scar tissue such as in the case of previous caesarean section. In this case report, a primigravid patient presented to the hospital in cardiac arrest with massive haemoperitoneum secondary to a posterior uterine rupture. The histological specimen was found to have diffuse adenomyosis at the site of rupture. On review of the literature, there is insufficient evidence to suggest we as clinicians should alter the antenatal care for patients with known adenomyosis; however, this case highlights how we should have a high index of suspicion for those presenting with signs and symptoms of uterine rupture with known adenomyosis in the absence of other risk factors.
Lung infarction secondary to infected pulmonary arterial thrombosis in a patient with Eisenmenger’s syndrome
Authors: Allan Liam , Shanks Anne-Marie , Polkey Mike
Published: December 2023

A case is presented where a patient with Eisenmenger’s syndrome is successfully treated for infection of chronic pulmonary arterial thrombosis with good effect. The evidence for antibiotic and anticoagulant therapy in this patient group is discussed.
Ethical and cultural implications for conducting verbal autopsies in South and Southeast Asia: a qualitative study
Authors: Htun Nan Shwe Nwe , Perrone Carlo , Phyo Aung Pyae , Sen Aninda , Phommasone Koukeo , Vanna Moul , Kanthawang Nipaphan , Sappayabanphot Jarntrah , Yotyingaphiram Widi , Wirachonphaophong Jindaporn , Kabir Nawrin , Ol Sam , Xaiyaphet Xaipasong , Soulivong Ailatda , Seevanhthong Khambang , Tripura Rupam , Chew Rusheng , Khirikoekkong Napat , Morris Shaun K , Osterrieder Anne , Cheah Phaik Yeong , Jha Prabhat , Lubell Yoel , Peto Thomas J
Published: December 2023

Introduction

Causes of deaths often go unrecorded in lower income countries, yet this information is critical. Verbal autopsy is a questionnaire interview with a family member or caregiver to elicit the symptoms and circumstances preceding a death and assign a probable cause. The social and cultural aspects of verbal autopsy have gotten less attention than the technical aspects and have not been widely explored in South and Southeast Asia settings.

Methods

Between October 2021 and March 2023, prior to implementing a verbal autopsy study at rural sites in Bangladesh, Cambodia, Laos, Myanmar and Thailand, focus group discussions were conducted with village heads, religious leaders and community members from varied demographic backgrounds. Thematic analysis elucidated customs and traditional views surrounding death to understand local ethnocultural sensitivities.

Results

We found that death rituals varied greatly among religions, ethnicities and by socioeconomic status. Mourning periods were reported to last 3–100 days and related to the cause of death, age and how close the deceased person was to the family. Participants advised that interviews should happen after mourning periods to avoid emotional distress, but not long after so as to avoid recall bias. Interviewers should be introduced to respondents by a trusted local person. To provide reassurance and confidentiality, a family’s residence is the preferred interview location. Interview questions require careful local language translation, and community sensitisation is important before data collection.

Conclusion

Verbal autopsy is acceptable across a wide range of cultural settings in Southeast Asia, provided that local norms are preidentified and followed.