bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization and prospective evaluation of sensitive real-time PCR assays with an internal control for the diagnosis of melioidosis in Thailand
Authors: Noparatvarakorn Chawitar , Jakkul Wallop , Seng Rathanin , Tandhavanant Sarunporn , Ottiwet Orawan , Janon Rachan , Saikong Wadsamon , Chantratita Narisara 
Published: October 2023

ABSTRACT

Melioidosis is a severe infectious disease caused by
Burkholderia pseudomallei
. Effective treatment of melioidosis requires rapid detection of
B. pseudomallei
infection. Previous studies demonstrated that real-time PCR for the diagnosis of melioidosis in blood samples was insensitive. We optimized the DNA extraction method and evaluated real-time PCRs with an internal control for the detection of
B. pseudomallei
in plasma samples and compared the performance of real-time PCRs based on six target genes. The lower limit of detection (LOD) of TTS1-
orf2
, BPSS0745, BPSS1187, and BPSS1498 real-time PCRs was ≤10 genome equivalent (GE)/reaction, while the LOD of BPSS0087 and BPSS1492 was 100 GE/reaction. In the initial phase, we evaluated four targets (TTS1-
orf2
, BPSS0745, BPSS1187, BPSS1498) for the diagnosis of melioidosis using 87 plasma samples from 38 bacteremic-melioidosis patients and 49 other infection patients at a hospital in Northeast Thailand. Among these, BPSS1187 exhibited the highest sensitivity of 76.3% and specificity of 100%. A second evaluation phase was conducted at two hospitals in Northeast Thailand to compare two real-time PCRs between BPSS1187 and widely used TTS1-
orf2
targets. A total of 705 clinical samples were collected from 421 suspected melioidosis cases; 77 of them were subsequently confirmed as melioidosis by culture using one or more specimens. The sensitivities of BPSS1187 and TTS1-
orf2
were 89.6% and 79.2%, respectively (
P
= 0.004), and the specificities were 96% and 99%, respectively. The sensitivities of these two assays in plasma samples were 84.6% and 67.7%, respectively (
P
= 0.007). Therefore, the BPSS1187 real-time PCR was sensitive and specific for early diagnosis of melioidosis.

IMPORTANCE

Melioidosis is a serious infectious disease caused by
Burkholderia pseudomallei
, an environmental Gram-negative bacterium. Early detection of
B. pseudomallei
infection is crucial for successful antibiotic treatment and reducing mortality rates associated with melioidosis. Bacteria culture is currently used to identify
B. pseudomallei
in clinical samples, but the method is slow. Therefore, there is a need for more accurate and sensitive molecular-based diagnostic methods that can detect
B. pseudomallei
in all sample types, including samples from blood. We developed an optimal DNA extraction method for
B. pseudomallei
from plasma samples and used an internal control for real-time PCR. We evaluated six PCR target genes and identified the most effective target for the early detection of
B. pseudomallei
infection in patients. To prevent delays in the treatment of melioidosis that can lead to fatal outcomes, we recommend implementing this new approach for routine early detection of
B. pseudomallei
in clinical settings.
Enhancing bacterial fitness and recombinant enzyme yield by engineering the quality control protease HtrA of
Bacillus subtilis
Authors: Öktem Ayşegül , Núñez-Nepomuceno David , Ferrero-Bordera Borja , Walgraeve Jonathan , Seefried Michael , Gesell Salazar Manuela , Steil Leif , Michalik Stephan , Maaß Sandra , Becher Dörte , Mäder Ulrike , Völker Uwe , van Dijl Jan Maarten 
Published: October 2023

ABSTRACT

Bacillus subtilis
is a Gram-positive bacterium that is well-known for its high secretory capacity. Although secretion of homologous proteins is extremely efficient, secretion of heterologous proteins imposes what is known as “secretion stress” on the cells. This is not desirable in an industrial setting, because the bacterial secretion stress responses can adversely affect product yields. So far, the main approach to reduce such counterproductive secretion stress responses has been to remove components of the CssR-CssS two-component regulatory system, including the CssR-CssS-regulated quality control proteases HtrA and/or HtrB. However, there are several examples indicating that a complete loss of these proteases does not correlate with improved protein secretion or a reduced secretion stress response. In this study, an alternative approach to limit the effects of secretion stress by modulating the protease activity of HtrA rather than completely removing this protease was investigated. Indeed, expression of the proteolytically inactive HtrA led to a generally improved fitness of the bacteria when producing the heterologous α-amylase AmyQ. Moreover, compared to control strains, the strain expressing the mutant HtrA provided higher AmyQ yields, which correlated with superior α-amylase enzymatic activity in shake flasks and fermenter-scale cultivations. Proteome analysis of the engineered strains revealed critical differences in stress responses and metabolism. Altogether, our present findings show how proteolytically inactive HtrA can be employed to achieve improved bacterial fitness and higher enzyme yields.

IMPORTANCE

In the expanding market of recombinant proteins, microbial cell factories such as
Bacillus subtilis
are key players. Microbial cell factories experience secretion stress during high-level production of secreted proteins, which can negatively impact product yield and cell viability. The CssRS two-component system and CssRS-regulated quality control proteases HtrA and HtrB play critical roles in the secretion stress response. HtrA has a presumptive dual function in protein quality control by exerting both chaperone-like and protease activities. However, its potential role as a chaperone has not been explored in
B. subtilis
. Here, we describe for the first time the beneficial effects of proteolytically inactive HtrA on α-amylase yields and overall bacterial fitness.
Lasso peptide MccY alleviates non-typhoidal salmonellae-induced mouse gut inflammation via regulation of intestinal barrier function and gut microbiota
Authors: Li Yu , Li Wenjing , Zeng Zhiwei , Han Yu , Chen Qinxi , Dong Xinyi , Wang Zepeng , Feng Saixiang , Cao Weisheng 
Published: October 2023

ABSTRACT

Non-typhoidal salmonellae-induced zoonotic intestinal bleeding infections are a crucial threat to public health worldwide, and the development of new medications is required to prevent and treat non-typhoid
Salmonella
(NTS) infections. MccY, a class of lasso peptide, is effective in biological sterilization against
Salmonella
and
Shigella
. In this study, the therapeutic effect of MccY on
S
. Typhimurium-infected BALB/c mice has been discussed. specific pathogen free (SPF) mice were infected with the ST53 strain with bacterial loads of 10
6
and 10
3
CFU/mL, respectively, and then treated with 9.92 mg/kg BW MccY. Results revealed that MccY significantly reduced mouse mortality by 20%–40% and effectively alleviated weight loss and diarrhea. The integrity of the intestinal structure was protected, and the expression of TNF-α, IL-6, IL-10, and IL-18 was inhibited. Particularly, MccY exerted multiple effects on gut microbiota ecology, including direct elimination of
Salmonella
, showing promise in limiting infection to the gut level and thereby halting the transmission of NTS. MccY indirectly inhibited other opportunistic pathogens and partially restored the microbiota, promoting an increase in
Bacteroidetes
,
Lactobacillus
,
Muribaculum
, and
Clostridium
. Consequently, this work provides an understanding of the link between host infection and therapeutic application of MccY.

IMPORTANCE

Diseases caused by
Enterobacteriaceae
multidrug-resistant strains have become increasingly difficult to manage. It is necessary to verify the new antibacterial drug MccY effect on non-typhoid
Salmonella
infection in mice since it is regarded as a promising microcin. The results demonstrated that MccY has a potential therapeutic application value in the protection against
Salmonella
-induced intestinal damage and alleviating related intestinal dysbiosis and metabolic disorders. MccY could be a promising candidate as an antimicrobial or anti-inflammatory agent for treating infectious diseases.
Protective efficacy of a candidate live attenuated vaccine derived from the SD-R strain of lineage 1 porcine reproductive and respiratory syndrome virus against a lethal challenge with HP-PRRSV HuN4 in piglets
Authors: Zhang Hongliang , Li Chao , Xu Hu , Gong Bangjun , Li Wansheng , Guo Zhenyang , Xiang Lirun , Sun Qi , Zhao Jing , Peng Jinmei , Wang Qian , Zhou Guohui , Tang Yan-Dong , An Tongqing , Cai Xue-Hui , Tian Zhi-Jun 
Published: October 2023

ABSTRACT

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen endangering the swine industry worldwide. Our previous study confirmed that the live attenuated vaccine SD-R strain could provide broad cross-protection against homologous and heterologous NADC30-like viruses. However, it is unclear whether SD-R can provide protection for piglets against HP-PRRSV. In the present study, 4-week-old PRRSV-free piglets were vaccinated intramuscularly with 10
6.2
TCID
50
of SD-R and then challenged intramuscularly (2 mL) and intranasally (2 mL) with HP-PRRSV HuN4 (1 × 10
5.0
TCID
50
/mL). The results showed that two of five piglets died in the HuN4 challenge group and five of five immunized piglets survived in the immune challenge group. Five piglets in the HuN4 challenge group had a fever for 6–12 days and showed obvious clinical symptoms, but 3 of 5 piglets had a fever for only 1 day at 5 days post inoculation, and only 1 of the 5 piglets in the immune challenge group had a cough. Compared to challenged control piglets, vaccinated piglets had significantly improved daily weight gain and obviously alleviated pathological lesions. Furthermore, piglets immunized with SD-R had reduced thymus atrophy caused by HP-PRRSV HuN4. These results demonstrate that the lineage 1 PRRSV attenuated vaccine SD-R strain provides protection against lethal HP-PRRSV HuN4 challenge. As such, it is a promising vaccine candidate for use against PRRSV infection.

IMPORTANCE
Both highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) and NADC30-like PRRSV have caused tremendous economic losses to the Chinese pig industry. In this study, a good challenge model was established to evaluate the protection afforded by the candidate SD-R vaccine against infection with a representative HP-PRRSV strain (HuN4). The control piglets in the challenge experiment displayed obvious clinical symptoms of PRRSV infection, with a mortality rate up to 40%. In contrast, all the piglets in the vaccinated challenged group survived, and only some pigs had transient fever. The daily gain of SD-R immunized group piglets was significantly increased, and the pathological changes were significantly reduced. In addition, the viral replication levels in the serum of the immunized group were significantly lower than those of the challenged control group. The live attenuated vaccine SD-R strain can provide protection against HP-PRRSV challenge, indicating that the SD-R strain is a promising vaccine candidate for use in the swine industry.
Emergence and genomic insights of non-pandemic O1
Vibrio cholerae
in Zhejiang, China
Authors: Luo Yun , Payne Michael , Kaur Sandeep , Octavia Sophie , Jiang Jianmin , Lan Ruiting 
Published: October 2023

ABSTRACT

Vibrio cholerae
O1 has caused cholera pandemics. Non-pandemic
V. cholerae
O1 strains, which are genetically distinctive from the pandemic clones, have been isolated from both human infections and the environment. We aimed to better understand the non-pandemic O1 strains and their pandemic potential. We sequenced 109 non-pandemic O1 isolates from Zhejiang, China (from 1963 to 1996) and compared them with 62 publicly available non-pandemic O1 genomes. The isolates from Zhejiang can be classified into three lineages (L1–L3). All grouped together with L3 sharing the most recent common ancestor with the pandemic clones. L2 and L3 emerged in the 1960s while L1 emerged in the 1970s. L1 and L2 disappeared after the 1990s, but L3 persisted until recently. All isolates contained the type VI secretion system. The
Vibrio
pathogenicity island was present in all L3 isolates, whereas the type III secretion system was present in all L1 isolates. L2 did not carry any unique virulence genes. An intact CTXφ was present in only two L3 isolates. An intact
Vibrio
seventh pandemic island 1 was present in only three L3 isolates. The

bla
CARB-7

gene was identified in 96.3% of L2 isolates. Each of the non-pandemic O1 lineages has unique properties contributing to their capacity to cause disease. Our findings offer new insight into the evolution of O1
V. cholerae
for cholera prevention and control.

IMPORTANCE

It is well recognized that only
Vibrio cholerae
O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1
V. cholerae
isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common ancestor with pandemic O1 strains. Each of these non-pandemic O1 lineages has unique properties that contribute to their capacity to cause cholera. The findings of this study enhanced our understanding of the emergence and evolution of both pandemic and non-pandemic O1
V. cholerae
.
The secreted tyrosine phosphatase PtpA promotes
Staphylococcus aureus
survival in RAW 264.7 macrophages through decrease of the SUMOylation host response
Authors: Youssouf Nadhuma , Martin Marianne , Bischoff Markus , Soubeyran Philippe , Gannoun-Zaki Laila , Molle Virginie 
Published: October 2023

ABSTRACT

Staphylococcus aureus
is a human pathogen that is extremely adaptable and is the cause of a variety of nosocomial and community-acquired infectious diseases. During infection,
S. aureus
is able to affect the host cell in many ways to enable its own multiplication, spread, and evasion of the host immune defense. One of the mechanisms utilized by
S. aureus
to survive is to inhibit the SUMOylation of host proteins in order to increase its intracellular survival and persistence. Here, we show that the reduction in the levels of cellular SUMO-conjugated proteins in
S. aureus
strain Newman-infected RAW 264.7 cells is associated with the
S. aureus
secreted protein tyrosine phosphatase PtpA, which results in a reduction of ubiquitin-conjugating enzyme 9 (Ubc9) protein level, the critical enzyme of the SUMOylation modification. In addition, we demonstrate that the amino acid residue D120, which is essential for PtpA phosphatase activity, is required for this reduction. This study shows for the first time that
S. aureus
strain Newman impedes via PtpA the host SUMOylation response, which contributes to promoting the persistence of
S. aureus
within the host.

IMPORTANCE

Staphylococcus aureus
uses numerous strategies to survive and persist in the intracellular environment of professional phagocytes, including modulation of the SUMOylation process. This study aims to understand how
S. aureus
alters host SUMOylation to enhance its intracellular survival in professional phagocytes. Our results indicate that
S. aureus
strain Newman utilizes PtpA-driven phosphorylation to decrease the amount of SUMOylated proteins in murine macrophages to facilitate its survival in this immune cell type.
A long-lived mafic magma reservoir: Zircon evidence from a hornblende peridotite in the Hida Belt, Japan
Authors: Itano Keita , Takehara Mami , Horie Kenji , Iizuka Tsuyoshi , Nishio Ikuya , Morishita Tomoaki 
Published: October 2023

Abstract
Zircon geochronology has contributed to our understanding of the longevity of transcrustal magmatic systems; however, most studies focus on zircon records from felsic rocks due to the restricted occurrence of zircon in mafic-ultramafic rocks. We present U–Pb age, geochemical, and Hf–O isotope data for zircons from a hornblendite peridotite in the Hida Belt, Japan, that offers a unique opportunity to investigate the lifetime of a long-lived mafic plumbing system in an arc setting. We found two zircon U–Pb age clusters: an incompatible element-rich cluster at 196 Ma and an incompatible element-poor cluster at 186 Ma. Their homogeneous isotopic signatures (δ18O = 7.7‰ ± 0.8‰, εHf = 10.3‰ ± 1.7‰) indicate the same magma source despite the 10 m.y. age gap. These two clusters are explained by different zircon formation mechanisms that differ depending on whether or not zircon saturation requires differentiated melt with high SiO2. The enriched older zircons formed by local zircon saturation at the mafic melt-olivine interface, whereas the younger depleted zircons precipitated from the last drop of interstitial felsic melt co-existing with hornblendes. Our finding substantiates the longevity of mafic systems at lower crusts, which sustain transcrustal magma systems and crustal evolution.
Ice-rafted dropstones at midlatitudes in the Cretaceous of continental Iberia
Authors: Rodríguez-López Juan Pedro , Liesa Carlos L. , Luzón Aránzazu , Muñoz Arsenio , Mayayo María J. , Murton Julian B. , Soria Ana R. 
Published: October 2023

Abstract
The Cretaceous is widely considered to have been a period subjected to super-greenhouse conditions. Here, we provide multiscale sedimentologic evidence of glaciers developing at mid-paleolatitudes (~45°N) in continental Iberia during the Hauterivian cold snap. Striated and faceted ice-rafted glacial dropstones (cobble to boulder size) and striated and grooved silt- to sand-sized grains (ice-rafted debris [IRD]) occur in a lacustrine sequence of the Enciso Group in the eastern Cameros Basin, Spain. The ice-rafted materials constitute the first evidence reported for a Cretaceous continental cryospheric record in Europe, and they are attributed to calving of glacier snouts, releasing icebergs into an ice-contact lake. The sedimentary succession resembles glacial-deglacial records in lakes overridden by the late Pleistocene Laurentide Ice Sheet in eastern Arctic Canada. The Iberian glacial succession was coeval with plateau permafrost in Asia and IRD records in the Arctic and Australia, revealing a stronger than previously thought cryosphere during the global Hauterivian cold snap.
Effects of combined physical and cognitive program performed in socially enriched environment on older people’s cognitive abilities and quality of life (StimCoAPS): study protocol for a randomized controlled trial
Authors: Gonnord Tiphanie , Clarys David ,   StimCoAPS Consortium, Dupuy Olivier , Albouy Marion , Migeot Virginie , Grangeiro Rebeca , Esnard Catherine , Boucard Geoffroy 
Published: October 2023

The number of older people worldwide is constantly increasing. However, ageing is accompanied by a decline in cognitive ability that can affect quality of life. Cognitive, physical and social activities can all slow this decline but social factors and their contribution to the well-being remain under-researched. The aim of this study is to analyse how the practice environment can foster these social relations and thus enhance well-being and to identify the psychological dimensions that are activated by social relations. This study is a 3-year randomised controlled trial designed to assess the effects on participants’ cognitive abilities and quality of life of a combined (ie, physical and cognitive) training programme in different social practice environments. A total of 159 older people (≥65 years old) will be recruited and randomly assigned to one of three practice environments: individual practice at home (n=53), group practice in a gymnasium (n=53) and group practice in an enriched environment (n=53). All participants will complete 12-week combined training sessions and will be assessed four times: before the start, in the middle, at the end and 6 months after the end of the programme. They will undergo cognitive function (episodic memory and executive functions), physical capacity (aerobic fitness, muscle strength and dynamic balance) and psychosocial assessments (indicators of psychological well-being, social support, self-esteem, anxiety, depression and achievement goal strategies), as well as semistructured interviews. Statistical analyses will be conducted to assess the effect of the practice environment on the perceived benefits of this programme in terms of cognitive abilities and quality of life, and to determine the role of psychosocial factors in this relationship.This protocol has been approved by an institutional review board (CERSTAPS: IRB00012476-2022-20-01-146). Trials registration number:NCT05721508.
Childhood contact with social services and risk of suicide or sudden death in young adulthood: identifying hidden risk in a population-wide cohort study
Authors: McKenna Sarah , O'Reilly Dermot , Maguire Aideen 
Published: October 2023

BackgroundChildhood out-of-home care is associated with premature death in adulthood, in particular death by suicide, accidents and violence. However, little is known about the mortality risk in the much larger population of adults that had contact with social services in childhood but never entered out-of-home care. We determine the association between all tiers of contact with children’s social services and risk of suicide and other sudden deaths in young adulthood.MethodsThis population-wide, longitudinal, record-linkage study of adults in Northern Ireland born between 1985 and 1997 (n=437 008) followed each individual from age 18 years to July 2021 (maximum age 36 years). Cox regression models estimated the association between level of contact with social services in childhood (no contact; referred but assessed as not in need (NIN); child in need (CIN) and child in care (CIC)) and risk of death by suicide and sudden death in young adulthood.ResultsIndividuals with childhood social care contact (n=51 097) comprised 11.7% of the cohort yet accounted for 35.3% of sudden deaths and 39.7% of suicide deaths. Risk of suicide or sudden death increased stepwise with level of childhood contact and was highest in adults with a history of out-of-home care (suicide HR 8.85 (95% CI 6.83 to 11.4)). Individuals assessed as NIN, and those deemed a CIN, had four times the risk of death by suicide in young adulthood compared with unexposed peers (HR 4.25 (95% CI 3.26 to 5.53) and HR 4.49 (95% CI 3.75 to 5.39), respectively).ConclusionChildhood contact with social services is a risk marker for death by suicide and sudden death in young adulthood. Risk is not confined to adults with a history of out-of-home care but extends to the much larger population that had contact with social services but never entered care.