bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulatory NADH dehydrogenase‐like complex optimizes C4 photosynthetic carbon flow and cellular redox in maize
Authors: Zhang Qiqi , Tian Shilong , Chen Genyun , Tang Qiming , Zhang Yijing , Fleming Andrew J. , Zhu Xin‐Guang , Wang Peng
Published: October 2023

C4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase‐like (NDH) complex is enriched in the BS cells of many NADP‐malic enzyme (ME) type C4 plants and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated.

We created maize and rice mutants deficient in NDH function and then used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis.

Considerable decreases in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, transcript abundance for many cyclic electron transport (CET) and Calvin–Benson cycle components, as well as BS‐specific C4 enzymes, was increased in maize mutants. Metabolite analysis of the maize ndh mutants revealed an increased NADPH : NADP ratio, as well as malate, ribulose 1,5‐bisphosphate (RuBP), fructose 1,6‐bisphosphate (FBP), and photorespiration intermediates.

We suggest that by optimizing NADPH and malate levels and adjusting NADP‐ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize (in addition to ATP supply), coordinating photosynthetic transcript abundance and protein content, thus directly regulating the carbon flow in the two‐celled C4 system of maize.
Treatment of Unstable Sacral Fractures with Robotically‐aided Minimally Invasive Triangular Fixation
Authors: Tian Wei , Jia Feng‐Shuang , Zheng Jia‐Ming , Jia Jian
Published: October 2023

Objective

The treatment of unstable sacral fractures is huge challenge to surgeons. Robotically‐aided minimally invasive triangular fixation (RoboTFX) is the most advanced technique up to now. This study is to evaluate the clinical outcomes of unstable sacral fractures treated with RoboTFX.

Methods

From March 2017 to October 2021, 48 consecutive patients with unstable sacral fractures were included in the study. All patients received surgical treatment with triangular fixation (TFX). Patients were divided into four groups according to the number of fractures (uni‐ or bilateral) and surgical method employed (RoboTFX or traditional open TFX). Between these four groups, clinical data on operation time, intraoperative bleeding, intraoperative fluoroscopy time, infection rate, fracture healing rates, insertion accuracy, Majeed pelvic outcome score, Mears' criterion, and Gibbons score were compared. Quantitative data were expressed as mean ± standard deviation and compared using Student's t‐test. Categorical variable were compared using the Pearson's χ2 test.

Results

Comparing unilateral RoboTFX versus open TFX, neither fracture healing rate, infection rate, Majeed pelvic outcome score, Mears' radiological evaluation criterion, nor Gibbons score of the two groups were statistically significantly different (p > 0.05). However, operation time, intraoperative bleeding, intraoperative fluoroscopy time, and insertion accuracy in the RoboTFX group were all significantly better than those of the traditional open group (p < 0.05). Likewise, operation time, intraoperative bleeding, intraoperative fluoroscopy time, and accuracy of fixation insertion of the bilateral RoboTFX group were significantly better than those of the bilateral open group (p < 0.05). Meanwhile infection rate, fracture healing rate, Majeed score, Mears' criterion, and Gibbons score of two groups were not significantly different (p > 0.05).

Conclusion

RoboTFX has the advantages of less operation time, less intraoperative bleeding and fluoroscopy, more accurate fixation insertion, and a higher healing rate compared to traditional open methods in the treatment of unstable sacral fractures. However, RoboTFX requires a few critical considerations, and the indications of its operation should be strictly evaluated.
Partisanship, Trump favorability, and changes in support for trade
Authors: Keser Ceren , Garand James C. , Xu Ping , Essig Joseph
Published: October 2023

Why has the relationship between partisan identification and Americans' trade attitudes shifted in recent years? We suggest that recent shifts in trade attitudes among partisans are driven by Donald Trump, who staked out a position on trade that is at odds with the position on trade traditionally held by Republicans. Using panel data from the Voter Study Group (VSG) surveys from 2011, 2016, and 2017, we conduct cross‐sectional analyses showing that the relationship between partisanship and trade attitudes has shifted dramatically from 2011 to 2016/2017; in 2011, Republicans were significantly more supportive of expanded trade, but by 2016/2017 the relationship had reversed, with Democrats significantly more supportive of trade. We link changes over time in trade attitudes with how Americans evaluate Trump: individuals with favorable attitudes toward Donald Trump are significantly more likely to shift their attitudes in an antitrade direction from 2011 to 2016. Because so many more Republicans have favorable attitudes toward Trump, the aggregate effect of Trump favorability is to shift Republicans as a group to be less favorable toward trade than Democrats. We suggest that Donald Trump has had a transformative effect on Americans' trade attitudes, with previous supporters (opponents) of expanded trade now expressing opposing (supporting) attitudes.
Spatiotemporal multi‐graph convolutional network‐based provincial‐day‐level terrorism risk prediction
Authors: Luo Lanjun , Li Boxiao , Qi Chao
Published: October 2023

Predicting terrorism risk is crucial for formulating detailed counter‐strategies. However, this task is challenging mainly because the risk of the concerned potential victim is not isolated. Terrorism risk has a spatiotemporal interprovincial contagious characteristic. The risk diffusion mechanism comes from three possibilities: cross‐provincial terrorist attacks, internal and external echoes, and internal self‐excitation. This study proposed a novel spatiotemporal graph convolutional network (STGCN)‐based extension method to capture the complex and multidimensional non‐Euclidean relationships between different provinces and forecast the daily risks. Specifically, three graph structures were constructed to represent the contagious process between provinces: the distance graph, the province‐level root cause similarity graph, and the self‐excited graph. The long short‐term memory and self‐attention layers were extended to STGCN for capturing context‐dependent temporal characters. At the same time, the one‐dimensional convolutional neural network kernel with the gated linear unit inside the classical STGCN can model single‐node‐dependent temporal features, and the spectral graph convolution modules can capture spatial features. The experimental results on Afghanistan terrorist attack data from 2005 to 2020 demonstrate the effectiveness of the proposed extended STGCN method compared to other machine learning prediction models. Furthermore, the results illustrate the crucial of capturing comprehensive spatiotemporal correlation characters among provinces. Based on this, this article provides counter‐terrorism management insights on addressing the long‐term root causes of terrorism risk and performing short‐term situational prevention.
Individual characteristics associated with perceptions of control over mortality risk and determinants of health effort
Authors: Brown Richard , Sillence Elizabeth , Pepper Gillian
Published: October 2023

People who believe they have greater control over health and longevity are typically more likely to invest in their long‐term health. Investigating individual differences in perceived control over risk and exploring different determinants of health effort may help to tailor health promotion programs to more effectively encourage healthy behaviors. From a sample of 1500 adults, we measured perceived control over 20 causes of death, overall perceived uncontrollable mortality risk (PUMR), state‐level optimism, self‐reported health effort, and the accuracy of estimations of avoidable deaths. We found individual differences in perceptions of control over specific causes of death based on age, gender, and income. PUMR was predicted by socioeconomic variables expected to influence exposure to risk and resource availability. Higher levels of PUMR, not perceptions of control over specific causes of death, predicted self‐reported health effort. The strength of relationship between PUMR and lower health effort was not moderated by state‐level optimism. Age and education both positively predicted greater accuracy in assessing the prevalence of avoidable deaths. We suggest that PUMR may capture people's “general sense” of mortality risk, influenced by both exposure to hazards and the availability of resources to avoid threats. Conversely, perceived control over specific risks may involve more deliberate, considered appraisals of risk. This general sense of risk is thought to play a more notable role in determining health behaviors than specific assessments of control over risk. Further study is needed to investigate the degree to which PUMR accurately reflects objective measures of individual risk.
Recreation and social obligations during Covid in India: Does social distancing act as a barrier?
Authors: Kaicker Nidhi , Gupta Aashi , Gaiha Raghav
Published: October 2023

Using three‐stage least squares, the present study examines how the household expenditure on socialising activities, including eating out, entertainment and religious and social obligations changed during the COVID‐19 pandemic in India. Our results suggest a negative impact of COVID‐19 cases on the socialising expenditure shares of the households. Further, a higher spending on food is associated with a lower spending on socialising. We find that during the crisis, the increased food expenditures entails lower discretionary expenditures. Or, in other words, they are substitutes. A quadratic socialising expenditures curve confirms the expenditure variability and the wide‐ranging responses of households belonging to different income groups to the COVID‐19 induced economic shocks. The rising prices of food and other necessities required the households to spend larger shares of their incomes on necessary goods, and curtail the consumption of leisure goods. The role of maintaining a healthy work‐life balance, active social network as well as leisure activities to be content in life is well documented. Hence a reduced expenditure on socialising due to the pandemic, may throw light on some larger and significant concerns such as the deteriorating mental health of individuals and greater stress and frustration.
Value‐added export tax policy, credit constraints, and quality: Evidence from China
Authors: Pernet Thomas
Published: October 2023

This paper examines the effect of an industrial policy in China named the VAT export tax on product upgrading. In particular, we use Chinese transaction data during 2003–2010 to isolate the causal impact of the exogenous variation of VAT refund and within the city‐product quality change in HS6 exported products. Our identification strategy entails the utilization of duality of the Chinese trade system to isolate the impact of the rebate by comparing a group of trade flows exempt from the refund and another that remains eligible. Our results suggest an increase in product upgrading in response to an increase in VAT refund. In this study, we also introduce the credit constraint to understand the change in quality. The industries that are confronted with tighter credit constraints impel firms to settle for low‐quality products. The model demonstrates that VAT refund provided a counterbalance force to credit constraints, thereby prompting firms to adjust quality. By increasing the refund granted to ordinary traders, firms leverage this excess cash flow to invest (in a fixed asset or innovative project) and improve the quality of products. This effect is reinforced for products exported to developed countries, heterogeneous products, or from larger industries. The Chinese policymakers formally introduced environmental objectives under the 10th and 11th FYP, respectively. The Party leaders put substantial weight on promoting products embedded with high‐added value or technological content. At the same time, they underscored the willingness to downscale the export share of energy‐intensive or polluting industries. We evaluate whether environmental and economic concern impacts product upgrading. According to the results of this study, the VAT refund is effective only for products produced in “cleaner” industries, for products necessitating technical skills, a range of know‐how in manufacturing, and high‐level technology or engaging in research and development activities. Our paper introduces a new and unexplored variable in the trade literature. We use the stock of non‐trade barriers to explicate the change in product quality. In the import market, Chinese exporters comply with the change in regulation by making upward adjustments in the quality.
Physical activity and endogenous pain modulation in older people: a scoping review protocol
Authors: Verbelen Debora , Korogod Natalya , Opsommer Emmanuelle
Published: October 2023

Objective:

This scoping review aims to provide an overview of the existing literature on physical activity and endogenous pain modulation (EPM), assessed using conditioned pain modulation (CPM), with a specific focus on older people with chronic pain.

Introduction:

Approximately 20% of the European population reports chronic pain, highlighting the problem of chronic pain in the general population. This prevalence increases to 50% in older people. Physical activity is one of the most frequently used treatments for pain management and relief. A possible mechanism underlying the positive effects of physical activity on pain may be related to its influence on EPM. The review will map i) types of physical activity used to study its effect on EPM in older people; ii) intervention protocols investigating physical activity and EPM, measured using CPM, in older people experiencing pain; and iii) knowledge gaps requiring further research or interventions adapted to older people with pain.

Inclusion criteria:

This review will consider studies of people aged 60 years or older, using CPM to examine the effect of physical activity on EPM. All types of care settings will be eligible.

Methods:

This review will be conducted in accordance with the JBI methodology for scoping reviews. The following databases will be searched: MEDLINE (Ovid), CINAHL (EBSCOhost), Embase, Cochrane Library, Web of Science, JBI Evidence Synthesis, PsycINFO, and PEDro.

Review registration:

Open Science Framework https://osf.io/e7ndy/
Muscle Mass and Strength Gains Following Resistance Exercise Training in Older Adults 65–75 Years and Older Adults Above 85 Years
Authors: Marzuca-Nassr Gabriel Nasri , Alegría-Molina Andrea , SanMartín-Calísto Yuri , Artigas-Arias Macarena , Huard Nolberto , Sapunar Jorge , Salazar Luis A. , Verdijk Lex B. , van Loon Luc J.C.
Published: October 2023

Resistance exercise training (RET) can be applied effectively to increase muscle mass and function in older adults (65–75 years). However, it has been speculated that older adults above 85 years are less responsive to the benefits of RET. This study compares the impact of RET on muscle mass and function in healthy older adults 65–75 years versus older adults above 85 years. We subjected 17 healthy older adults 65–75 years (OLDER 65–75, n = 13/4 [female/male]; 68 ± 2 years; 26.9 ± 2.3 kg/m2) and 12 healthy older adults above 85 years (OLDER 85+, n = 7/5 [female/male]; 87 ± 3 years; 26.0 ± 3.6 kg/m2) to 12 weeks of whole-body RET (three times per week). Prior to, and after 6 and 12 weeks of training, quadriceps and lumbar spine vertebra 3 muscle cross-sectional area (computed tomography scan), whole-body lean mass (dual-energy X-ray absorptiometry scan), strength (one-repetition maximum test), and physical performance (timed up and go and short physical performance battery) were assessed. Twelve weeks of RET resulted in a 10% ± 4% and 11% ± 5% increase in quadriceps cross-sectional area (from 46.5 ± 10.7 to 51.1 ± 12.1 cm2, and from 38.9 ± 6.1 to 43.1 ± 8.0 cm2, respectively; p < .001; η2 = .67); a 2% ± 3% and 2% ± 3% increase in whole-body lean mass (p = .001; η2 = .22); and a 38% ± 20% and 46% ± 14% increase in one-repetition maximum leg extension strength (p < .001; η2 = .77) in the OLDER 65–75 and OLDER 85+ groups, respectively. No differences in the responses to RET were observed between groups (Time × Group, all p > .60; all η2 ≤ .012). Physical performance on the short physical performance battery and timed up and go improved (both p < .01; η2 ≥ .22), with no differences between groups (Time × Group, p > .015; η2 ≤ .07). Prolonged RET increases muscle mass, strength, and physical performance in the aging population, with no differences between 65–75 years and 85+ years older adults.
A New Way to Restrict Free Leg Movement During Unilateral Vertical Jump Test
Authors: Schmidt Christian , Perroulaz Mike , Perez Yago , Rosset Jérémie , Wüthrich Gabriel , Malatesta Davide , Samozino Pierre
Published: October 2023

The purpose of this investigation was (1) to test the effect of movement restriction of the free leg during unilateral vertical jump on performance and power output comparing 2 different jump techniques: flexed (Classic technique) and straight (FC Luzern technique) free leg, and (2) to test the correlation between performance and power output obtained using these 2 techniques. Twenty elite soccer players performed squat (SJ) and countermovement (CMJ) jumps on each leg. The jump height and peak power output were compared between the 2 techniques for both legs. The jump height and peak power were significantly higher for the classic test for SJ and CMJ (P < .001) with no side effects or interactions. The angular range of motion of the free leg was higher for the Classic test than for the FC Lucerne test (P < .001), with no difference in the angular range of motion of the trunk. A moderate correlation was found between the 2 techniques on peak power (SJ: r = .626; CMJ: r = .649) and jump height (SJ: r = .742; CMJ: r = .891). Consequently, FC Lucerne technique, limiting the contribution of the free leg, is more appropriate to assess lower limb strength capacities during unilateral jump test.
Routine ophthalmologic examination in
Klebsiella pneumoniae
bacteremia is not necessary: incidence of and risk factors for ocular involvement
Authors: Lim So Yun , Kwon Hye Ji , Lee Yun Woo , Sung Heungsup , Kim Mi-Na , Chang Euijin , Bae Seongman , Jung Jiwon , Kim Min Jae , Kim Sung-Han , Choi Sang-Ho , Lee Sang-Oh , Kim Yang Soo , Lee Joo Yong , Chong Yong Pil
Published: October 2023

Klebsiella pneumoniae
bacteremia is known to present a virulent clinical course, including multiple metastatic infections, which is not uncommon in Asia. However, there are limited data on the incidence and risk factors for ocular involvement in
K. pneumoniae
bacteremia. We retrospectively reviewed the medical records of all patients with
K. pneumoniae
bacteremia who underwent ophthalmologic examination in a tertiary center in Seoul, Korea, from February 2012 to December 2020. Two retinal specialists reviewed the findings of the ophthalmologic examinations and classified them as endophthalmitis, chorioretinitis, and no ocular involvement. Of 689 patients, 56 [8.1%; 95% confidence interval (CI) 6.2–10.4] had ocular involvement, and 9 (1.3%; 95% CI 0.6–2.5) were diagnosed with endophthalmitis. Of 47 patients with chorioretinitis, 45 (95.7%) improved with systemic antibiotic therapy alone. Community-onset bacteremia (100% vs 62.1% vs 57.4%,
P
= 0.04), cryptogenic liver abscess (55.6% vs 11.8% vs 8.5%,
P
= 0.003), and metastatic infection (66.7% vs 5.8% vs 10.6%,
P
< 0.001) were more common in endophthalmitis than in no ocular involvement or chorioretinitis. In the multivariable analysis, cryptogenic liver abscess [adjusted odds ratio (aOR), 6.63; 95% CI 1.44–35.20] and metastatic infection (aOR, 17.52; 95% CI 3.69–96.93) were independent risk factors for endophthalmitis. Endophthalmitis was not associated with 30-day mortality. Endophthalmitis is rare in Asian patients with
K. pneumoniae
bacteremia. Targeted ophthalmologic examination in those with cryptogenic liver abscess, metastatic infection, or ocular symptoms may be more appropriate than routine examination of all patients.
Characterization of thraustochytrid-specific sterol
O
-acyltransferase: modification of DGAT2-like enzyme to increase the sterol production in
Aurantiochytrium limacinum
mh0186
Authors: Ishibashi Yohei , Sadamitsu Shohei , Fukahori Yoshitomo , Yamamoto Yuki , Tanogashira Rin , Watanabe Takashi , Hayashi Masahiro , Ito Makoto , Okino Nozomu
Published: October 2023

Thraustochytrids are marine microorganisms expected to produce useful lipids. They synthesize polyunsaturated fatty acids and sterols and store them in lipid droplets as a form of triacylglycerol (TG) and sterol ester (SE), respectively. TG is synthesized by diacylglycerol
O
-acyltransferase (DGAT). There are several DGAT2 homologs in
Aurantiochytrium limacinum
. This study indicated that DGAT2C and DGAT2D are SE synthase and TG synthase, respectively, by disrupting their corresponding genes in
A. limacinum
mh0186. DGAT2C is revealed as thraustochytrid-specific acyl-CoA:sterol-
O
-acyltransferase by performing
in vivo
and
in vitro
assays after heterologous expression in
Saccharomyces cerevisiae
. DGAT2C and DGAT2D localized mainly to the endoplasmic reticulum (ER) and the lipid droplet, respectively, and the two of the N-terminal domains unique to DGAT2C were essential for ER localization and SE synthesis in
A. limacinum
mh0186. Interestingly, the study also found that deletion of the first eight transmembrane domains in the unique N-terminal region of DGAT2C increased SE and total sterol productivity when expressed in DGAT2C-deficient
A. limacinum
mh0186. In addition, intermediates such as Δ7-cholesterol (provitamin D3) also accumulated in SE by expression of the N-terminal-truncated DGAT2C, along with cholesterol and Δ7-stigmasterol, a major phytosterol in
A. limacinum
. This study proves that DGAT2C is an ER-localized SE synthase and that its suitable N-terminal deletion can increase sterol production in thraustochytrids.

IMPORTANCE

Since the global market for sterols and vitamin D are grown with a high compound annual growth rate, a sustainable source of these compounds is required to keep up with the increasing demand. Thraustochytrid is a marine oleaginous microorganism that can synthesize several sterols, which are stored as SE in lipid droplets. DGAT2C is an unconventional SE synthase specific to thraustochytrids. Although the primary structure of DGAT2C shows high similarities with that of DGAT, DGAT2C utilizes sterol as an acceptor substrate instead of diacylglycerol. In this study, we examined more detailed enzymatic properties, intracellular localization, and structure-activity relationship of DGAT2C. Furthermore, we successfully developed a method to increase sterol and provitamin D3 productivity of thraustochytrid by more than threefold in the process of elucidating the function of the DGAT2C-specific N-terminal region. Our findings could lead to sustainable sterol and vitamin D production using thraustochytrid.
Active viral infection during blooms of a dinoflagellate indicates dinoflagellate-viral co-adaptation
Authors: Wang Jingtian , Li Ling , Lin Senjie
Published: October 2023

Viruses are generally believed to cause cell mortality and terminate algal blooms. However, how the dinoflagellate-virus interaction shapes the dynamics of host dinoflagellate blooms remains poorly understood. Here, we profile viral composition and metabolic landscape in two blooms of the widely distributed dinoflagellate
Prorocentrum shikokuense
. Our data show that
P. shikokuense
was infected dominantly by
Mimiviridae
and
Phycodnaviridae
viruses in both blooms. Strikingly, these viruses were transcriptionally very active during the bloom that extended for weeks, suggesting a paralleled development of both the bloom and chronic infection. Furthermore, our data indicate that these viruses maintained a stable infection process by generating polymorphic variants to sustain the exploitation of host intracellular machinery, suggesting co-adaptation between the viruses and the bloom-causative dinoflagellate. This novel insight will be valuable for fully understanding and modeling the role of viruses in regulating blooms of dinoflagellates and other algae.

IMPORTANCE

This study represents the first that investigates
in situ
virus infection in dinoflagellate blooms. Our findings reveal highly similar viral assemblages that infected the bloom species
Prorocentrum shikokuense
and a co-adapted metabolic relationship between the host and the viruses in the blooms, which varied between the prolonged and the short-lived blooms of the same dinoflagellate species. These findings fill the gap in knowledge regarding the identity and behavior of viruses in a dinoflagellate bloom and shed light on what appears to be the complex mode of infection. The novel insight will be potentially valuable for fully understanding and modeling the role of viruses in regulating blooms of dinoflagellates and other algae.
Effects of
Trichinella spiralis
and its serine protease inhibitors on autophagy of host small intestinal cells
Authors: Zhen Jing-Bo , Wang Rui-Biao , Zhang Yu-Heng , Sun Feng , Lin Li-Hao , Li Zhi-Xin , Han Yang , Lu Yi-Xin
Published: October 2023

In eukaryotes, autophagy is induced as an innate defense mechanism against pathogenic microorganisms by self-degradation. Although trichinellosis is a foodborne zoonotic disease, there are few reports on the interplay between
Trichinella spiralis
survival strategies and autophagy-mediated host defense. Therefore, this study focused on the association between
T. spiralis
and autophagy of host small intestinal cells. In this study, the autophagy-related indexes of host small intestinal cells after
T. spiralis
infection were detected using transmission electron microscopy, hematoxylin and eosin staining, immunohistochemistry, quantitative real-time polymerase chain reaction, and Western blotting. The results showed that autophagosomes and autolysosomes were formed in small intestinal cells, intestinal villi appeared edema, epithelial compactness was decreased, microtubule-associated protein 1A/1B-light chain 3B (LC3B) was expressed in lamina propria stromal cells of small intestine, and the expression of autophagy-related genes and proteins was changed significantly, indicating that
T. spiralis
induced autophagy of host small intestinal cells. Then, the effect of
T. spiralis
on autophagy-related pathways was explored by Western blotting. The results showed that the expression of autophagy-related pathway proteins was changed, indicating that
T. spiralis
regulated autophagy by affecting autophagy-related pathways. Finally, the roles of
T. spiralis
serine protease inhibitors (
Ts
SPIs), such as
T. spiralis
Kazal-type SPI (
Ts
KaSPI) and
T. spiralis
Serpin-type SPI (
Ts
AdSPI), were further discussed
in vitro
and
in vivo
experiments. The results revealed that
Ts
SPIs induced autophagy by influencing autophagy-related pathways, and
Ts
AdSPI has more advantages. Overall, our results indicated that
T. spiralis
induced autophagy of host small intestinal cells, and its
Ts
SPIs play an important role in enhancing autophagy flux by affecting autophagy-related pathways. These findings lay a foundation for further exploring the pathogenesis of intestinal dysfunction of host after
T. spiralis
infection, and also provide some experimental and theoretical basis for the prevention and treatment of trichinellosis
.
The Rrp2-RpoN-RpoS pathway plays an important role in the blood-brain barrier transmigration of the Lyme disease pathogen
Authors: Alanazi Fuad , Raghunandanan Sajith , Priya Raj , Yang X. Frank
Published: October 2023

Lyme disease, caused by
Borrelia
(or
Borreliella
)
burgdorferi
, is a complex multisystemic disorder that includes Lyme neuroborreliosis resulting from the invasion of both the central and peripheral nervous systems. However, factors that enable the pathogen to cross the blood-brain barrier (BBB) and invade the central nervous system (CNS) are still not well understood. The objective of this study was to identify the
B. burgdorferi
factors required for BBB transmigration. We utilized a transwell BBB model based on human brain-microvascular endothelial cells and focused on investigating the Rrp2-RpoN-RpoS pathway, a central regulatory pathway that is essential for mammalian infection by
B. burgdorferi
. Our results demonstrated that the Rrp2-RpoN-RpoS pathway is crucial for BBB transmigration. Furthermore, we identified OspC, a major surface lipoprotein controlled by the Rrp2-RpoN-RpoS pathway, as a significant contributor to BBB transmigration. Constitutive production of OspC in a mutant defective in the Rrp2-RpoN-RpoS pathway did not rescue the impairment in BBB transmigration, indicating that this pathway controls additional factors for this process. Two other major surface lipoproteins controlled by this pathway, DbpA/B and BBK32, appeared to be dispensable for BBB transmigration. In addition, both the surface lipoprotein OspA and the Rrp1 pathway, which are required
B. burgdorferi
colonization in the tick vector, were found not required for BBB transmigration. Collectively, our findings using
in vitro
transwell assays uncover another potential role of the Rrp2-RpoN-RpoS pathway in BBB transmigration of
B. burgdorferi
and invasion into the CNS.
Detoxification of reactive oxygen species by the hyaluronic acid capsule of group A
Streptococcus
Authors: Wilde Shyra , Dash Ananya , Johnson Anders , Mackey Kialani , Okumura Cheryl Y. M. , LaRock Christopher N.
Published: October 2023

The pro-inflammatory cytokine IL-6 regulates antimicrobial responses that are broadly crucial in the defense against infection. Our prior work shows that IL-6 promotes the killing of the M4 serotype group A
Streptococcus
(GAS) but does not impact the globally disseminated M1T1 serotype associated with invasive infections. Using
in vitro
and
in vivo
infection models, we show that IL-6 induces phagocyte reactive oxygen species (ROS) that are responsible for the differential susceptibility of M4 and M1T1 GAS to IL-6-mediated defenses. Clinical isolates naturally deficient in capsule, or M1T1 strains deficient in capsule production, are sensitive to this ROS killing. The GAS capsule is made of hyaluronic acid, an antioxidant that detoxifies ROS and can protect acapsular M4 GAS when added exogenously. During
in vitro
interactions with macrophages and neutrophils, acapsular GAS can also be rescued with the antioxidant N-acetylcysteine, suggesting this is a major virulence contribution of the capsule. In an intradermal infection model with

gp91
phox

-/-
(chronic granulomatous disease [CGD]) mice, phagocyte ROS production had a modest effect on bacterial proliferation and the cytokine response but significantly limited the size of the bacterial lesion in the skin. These data suggest that the capsule broadly provides enhanced resistance to phagocyte ROS but is not essential for invasive infection. Since capsule-deficient strains are observed across several GAS serotypes and are competent for transmission and both mild and invasive infections, additional host or microbe factors may contribute to ROS detoxification during GAS infections.
A cost-free CURE: using bioinformatics to identify DNA-binding factors at a specific genomic locus
Authors: Schmidt Casey A. , Hodkinson Lauren J. , Comstra H. Skye , Khan Samia , Torres Henrik , Rieder Leila E.
Published: October 2023

Research experiences provide diverse benefits for undergraduates. Many academic institutions have adopted course-based undergraduate research experiences (CUREs) to improve student access to research opportunities. However, potential instructors of a CURE might still face financial or practical hurdles that prevent implementation. Bioinformatics research offers an alternative that is free, safe, compatible with remote learning, and may be more accessible for students with disabilities. Here, we describe a bioinformatics CURE that leverages publicly available datasets to discover novel proteins that target an instructor-determined genomic locus of interest. We use the free, user-friendly bioinformatics platform Galaxy to map ChIP-seq datasets to a genome, which removes the computing burden from students. Both faculty and students directly benefit from this CURE, as faculty can perform candidate screens and publish CURE results. Students gain not only basic bioinformatics knowledge, but also transferable skills, including scientific communication, database navigation, and primary literature experience. The CURE is flexible and can be expanded to analyze different types of high-throughput data or to investigate different genomic loci in any species.
Draft genome sequence of
Pseudomonas
sp. ER28, a cyclohexane pentanoic acid degrader isolated from oil sands process-affected water from Alberta, Canada
Authors: Goff Kira L. , Gauthier Jeff , Gieg Lisa M. , Kukavica-Ibrulj Irena , Ramos-Padrón Esther , Lewenza Shawn , Levesque Roger C.
Published: October 2023

We report the draft genome sequence of
Pseudomonas
sp. ER28, capable of utilizing the model naphthenic acid, cyclohexane pentanoic acid, as its sole carbon source. It was recovered from oil sands process-affected water containing cyclic and acyclic naphthenic acids. The genome size is 5.7 Mbp, and the G + C content is 60%.
Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts
Authors: Vänni Petri , Tejesvi Mysore V. , Paalanne Niko , Aagaard Kjersti , Ackermann Gail , Camargo Carlos A. , Eggesbø Merete , Hasegawa Kohei , Hoen Anne G. , Karagas Margaret R. , Kolho Kaija-Leena , Laursen Martin F. , Ludvigsson Johnny , Madan Juliette , Ownby Dennis , Stanton Catherine , Stokholm Jakob , Tapiainen Terhi
Published: October 2023

Combining and comparing microbiome data from distinct infant cohorts has been challenging because such data are inherently multidimensional and complex. Here, we used an ensemble of machine-learning (ML) models and studied 16S rRNA amplicon sequencing data from 4,099 gut microbiome samples representing 12 prospectively collected infant cohorts. We chose the childbirth delivery mode as a starting point for such analysis because it has previously been associated with alterations in the gut microbiome in infants. In cross-study ensemble models, Bacteroides was the most important feature in all machine-learning models. The predictive capacity by taxonomy varied with age. At the age of 1–2 months, gut microbiome data were able to predict delivery mode with an area under the curve of 0.72 to 0.83. In contrast, ML models trained on taxa were not able to differentiate between the modes of delivery, in any of the cohorts, when the infants were between 3 and 12 months of age. Moreover, no ML model, alternately trained on the functional pathways of the infant gut microbiome, could consistently predict mode of delivery at any infant age. This study shows that infant gut microbiome data sets can be effectively combined with the application of ML analysis across different study populations.

IMPORTANCE

There are challenges in merging microbiome data from diverse research groups due to the intricate and multifaceted nature of such data. To address this, we utilized a combination of machine-learning (ML) models to analyze 16S sequencing data from a substantial set of gut microbiome samples, sourced from 12 distinct infant cohorts that were gathered prospectively. Our initial focus was on the mode of delivery due to its prior association with changes in infant gut microbiomes. Through ML analysis, we demonstrated the effective merging and comparison of various gut microbiome data sets, facilitating the identification of robust microbiome biomarkers applicable across varied study populations.
Characterization of spatial lipidomic signatures in tick-bitten guinea pig skin as a model for host-vector-pathogen interaction profiling
Authors: Scott Alison J. , Smith Alexis A. , Heeren Ron M. A. , Pal Utpal , Ernst Robert K.
Published: October 2023

Spatially aware
de novo
discovery methods are essential tools for therapeutic target identification in complex interphylum interactions such as arthropods and mammals. Notably, the methods should ideally be species agnostic, showing unique features of all interacting species. We evaluated the possibilities for matrix-assisted desorption/ionization mass spectrometry imaging (MALDI-MSI, referred to here as MSI) as a spatial “omics” method to simultaneously profile both an arthropod vector (
Ixodes
tick) and a mammalian skin (guinea pig) in a bite model. We demonstrated the feasibility of MSI using gelatin-stabilized sample mounting that allowed for serial sectioning and mapping lipids in control and bitten skin, including the tick body and embedded mouthparts. We identified unique lipid ion patterns and observed lipid reorganization beneath the bite site consistent with histological changes. Furthermore, several ions were observed in the tick body with lower intensity in the dermis and control skin, suggesting the transmission of lipids from the tick to mammalian skin. These results establish a multi-system approach for discovering cross-species molecular interactions that can be further developed as targets to disrupt the vector-host interface.

IMPORTANCE

Here, we demonstrate the adaptability of spatial “omics” methods to identify interphylum processes regulated at the vector-host interface of ticks during a mammalian blood meal. This approach enables a better understanding of complex bipartite or tripartite molecular interactions between hosts, arthropod vectors and transmitted pathogens, and contributes toward the development of spatially aware therapeutic target discovery and description.
Clinically relevant mutations in the PhoR sensor kinase of host-adapted
Mycobacterium abscessus
isolates impact response to acidic pH and virulence
Authors: Belardinelli Juan M. , Arora Divya , Avanzi Charlotte , Wheat William H. , Bryant Josephine M. , Spencer John S. , Blundell Tom L. , Parkhill Julian , Floto R. Andres , Jackson Mary
Published: October 2023

Functional genomics analysis of
Mycobacterium abscessus
clinical isolates from chronically infected patients to identify genes under strong evolutionary pressure during lung adaptation identified
phoR
as one of the most frequently mutated.
phoR
encodes the histidine kinase (HK) of the two-component regulatory system (TCS) PhoPR. While PhoPR has been extensively studied in
Mycobacterium tuberculosis
for its role in virulence, little is known about the function of this TCS and the signals governing its activation in
M. abscessus
. We here show that acidic pH leads to the upregulation of
phoP
in
M. abscessus
and that clinically relevant non-synonymous mutations identified in PhoR exacerbate this response. PhoR modulates the ability of its cognate response regulator, PhoP, to autoregulate itself by controlling its dephosphorylation. At low pH, the phosphatase activity of PhoR is reduced and the build-up of phospho-PhoP that ensues results in the upregulation of
phoP
that accompanies the induction of a defined set of genes, many of which are thought to play a role in virulence and host adaptation. In line with the idea that
M. abscessus
isolates expressing clinically relevant PhoR variants may be better prepared for survival within the host, we find these strains to be less efficiently internalized by macrophages and to display enhanced intracellular survival.

IMPORTANCE

Difficult-to-treat pulmonary infections caused by nontuberculous mycobacteria of the
Mycobacterium abscessus
group have been steadily increasing in the USA and globally. Owing to the relatively recent recognition of
M. abscessus
as a human pathogen, basic and translational research to address critical gaps in diagnosis, treatment, and prevention of diseases caused by this microorganism has been lagging behind that of the better-known mycobacterial pathogen,
Mycobacterium tuberculosis
. To begin unraveling the molecular mechanisms of pathogenicity of
M. abscessus
, we here focus on the study of a two-component regulator known as PhoPR which we found to be under strong evolutionary pressure during human lung infection. We show that PhoPR is activated at acidic pH and serves to regulate a defined set of genes involved in host adaptation. Accordingly, clinical isolates from chronically infected human lungs tend to hyperactivate this regulator enabling
M. abscessus
to escape macrophage killing.
Systematic investigation of the emerging pathogen of
Tsukamurella
species in a Chinese tertiary teaching hospital
Authors: Yu Shuying , Ding Xiaoqi , Hua Kexin , Zhu Huiqing , Zhang Qingshui , Song Xinuo , Xie Xiuli , Huang Rong , Xu Yingchun , Zhang Li , Yi Qiaolian , Zhao Ying
Published: October 2023

Tsukamurella
species have been clinically regarded as rare but emerging opportunistic pathogens causing various infections in humans.
Tsukamurella
pneumonia has often been misdiagnosed as pulmonary tuberculosis due to its clinical presentation resembling tuberculosis-like syndromes.
Tsukamurella
species have also been confused in the laboratory with other phylogenetic bacteria, such as
Gordonia
. This study aimed to investigate the clinical, microbiological, and molecular characteristics; species distribution; and antimicrobial susceptibility of
Tsukamurella
species. Immunodeficiency and chronic pulmonary disease appeared to be risk factors for
Tsukamurella
pneumonia, and the presence of bronchiectasis and pulmonary nodules on imaging was highly correlated with this infection. The study confirmed that
groEL
(heat shock protein 60) and
secA
(the secretion ATPase) genes are reliable for identifying
Tsukamurella
species. Additionally, the
ssrA
(stable small RNA) gene showed promise as a tool for discriminating between different
Tsukamurella
species with the shortest sequence length. In terms of antimicrobial susceptibility, quinolones, trimethoprim/sulfamethoxazole, amikacin, minocycline, linezolid, and tigecycline demonstrated potent
in vitro
activity against
Tsukamurella
isolates in our study. The study also proposed a resistance mechanism involving a substitution (S91R) within the quinolone-resistance-determining region of the
gyrA
gene, which confers resistance to levofloxacin and ciprofloxacin. Furthermore, we found that disk diffusion testing is not suitable for testing the susceptibilities of
Tsukamurella
isolates to ciprofloxacin, imipenem, and minocycline. In conclusion, our systematic investigation may contribute to a better understanding of this rare pathogen.

Tsukamurella
species are rare but emerging human pathogens that share remarkable similarities with other mycolic acid–containing genera of the order Actinomycetales, especially
Mycobacterium tuberculosis
. Consequently, misdiagnosis and therapeutic failures can occur in clinical settings. Despite the significance of accurate identification, antimicrobial susceptibility, and understanding the resistance mechanism of this important genus, our knowledge in these areas remains fragmentary and incomplete. In this study, we aimed to address these gaps by investigating promising identification methods, the antimicrobial susceptibility patterns, and a novel quinolone resistance mechanism in
Tsukamurella
species, utilizing a collection of clinical isolates. The findings of our study will contribute to improve diagnosis and successful management of infections caused by
Tsukamurella
species, as well as establishing well-defined performance and interpretive criteria for antimicrobial susceptibility testing.
Culture-independent analyses of carrion beetle (Coleoptera: Silphidae) secretion bacterial communities
Authors: Pratt Carrie J. , Meili Casey H. , Youssef Noha H. , Hoback W. Wyatt
Published: October 2023

In the central plains of North America, the beetle family Silphidae comprised two subfamilies, Silphinae and Nicrophorinae, differentiated by reproductive behaviors. Silphinae, known as carrion beetles, feed on carrion and fly larvae and produce free-living larvae that receive no parental care. Adult Nicrophorinae, known as burying beetles, prepare a vertebrate carcass into a brood ball and provide biparental care to their offspring. Preparation of a brood ball involves coating the carcass in antimicrobial oral and anal secretions. These secretions contain a community of microbes, referred to as the secretion microbiome, which inhibit carcass microbe succession, preventing normal decomposition. Here, the secretion microbiomes of five species of Nicrophorinae and two species of Silphinae, both sampled from Oklahoma, with additional Nicrophorinae from Nebraska, were characterized using culture-independent analyses to understand and decipher factors shaping diversity and community structure. We identify the core secretion microbiome across Silphidae and show that, while the host subfamily, secretion type, and collection locality had no significant effect on the bacterial community alpha diversity, these factors significantly influenced bacterial community structure. Global and local tests of phylogenetic associations identified 14 genera with phylogenetic signals to the host subfamily and species. Description of the bacterial communities present in silphid secretions furthers our understanding of how these beetles interact with microbes for carcass nutrient processing. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.

IMPORTANCE

The manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.