Hierarchical classification of functionally equivalent genes in prokaryotes

Functional classification of genes represents a fundamental problem to many biological studies. Most of the existing classification schemes are based on the concepts of homology and orthology, which were originally introduced to study gene evolution but might not be the most appropriate for gene function prediction, particularly at high resolution level. We have recently developed a scheme for hierarchical classification of genes (HCGs) in prokaryotes. In the HCG scheme, the functional equivalence relationships among genes are first assessed through a careful application of both sequence similarity and genomic neighborhood information; and genes are then classified into a hierarchical structure of clusters, where genes in each cluster are functionally equivalent at some resolution level, and the level of resolution goes higher as the clusters become increasingly smaller traveling down the hierarchy. The HCG scheme is validated through comparisons with the taxonomy of the prokaryotic genomes, Clusters of Orthologous Groups (COGs) of genes and the Pfam system. We have applied the HCG scheme to 224 complete prokaryotic genomes, and constructed a HCG database consisting of a forest of 5339 multi-level and 15 770 single-level trees of gene clusters covering approximately 93% of the genes of these 224 genomes. The validation results indicate that the HCG scheme not only captures the key features of the existing classification schemes but also provides a much richer organization of genes which can be used for functional prediction of genes at higher resolution and to help reveal evolutionary trace of the genes.     

富贵草杀灭钉螺效应研究

以富贵草(Pachysandra terminalis Sieb.et Zucc.)(以下简称PT)为实验材料,采用开放式浸杀法研究其植物原粉及提取物(PT-Ⅰ)对钉螺的杀灭效果和对鱼类的毒性作用。结果表明PT原粉浓度为17.5 mg/L时,钉螺72 h死亡率为93.4%,120 h死亡率达100.0%;其24、72、120、168 h的LC50分别为42.28、7.20、4.20、3.17 mg/L。PT原粉浓度为75.0 mg/L时,经168 h鱼死亡率为0。使用浓度为35.0、17.5、8.75、4.38 mg/L的PT原粉,分别浸泡1、2、18、42 h时,抑制钉螺上爬率均达到100%。原粉经提取分离得到PT-Ⅰ组分,以1.40 mg/L的PT-Ⅰ组分分别浸杀钉螺24、48、72、96、120 h,钉螺死亡率分别为36.7%、73.3%、96.7%、96.7%、100.0%。表明PT具有很好的杀灭钉螺、抑制钉螺上爬效果,且对鱼毒性较低,是一种较有研究价值的灭螺植物。     

剩余活性污泥完全资源化利用微生物集成技术

剩余活性污泥完全资源化利用微生物集成技术包括: 使用土著PHA合成菌回注法驯化并发酵活性污泥, 生产生物降解材料聚羟基脂肪酸酯(PHA); 采用土著嗜酸性氧化亚铁硫杆菌和氧化硫硫杆菌进行生物淋滤, 去除重金属; 以解磷菌和解钾菌为菌种, 进行固态发酵, 生产生物菌肥。结果表明, 500 L中试PHA占挥发性悬浮固体的20%以上; 重金属含量达到国家排放要求; 生物菌肥中活菌数大于1×108 个/g以上。实现了剩余活性污泥的近零排放。     

模拟增温对杉木幼树生长和光合特性的影响

为阐明杉木生长特征及光合能力对未来全球变暖的响应方式,通过在福建省三明市森林生态系统与全球变化研究站陈大观测点内开展的土壤增温(电缆加热,+4℃)实验,研究了增温条件下杉木幼树生长(树高、地径)特征及光合作用参数的变化,并对土壤有效氮(N)、叶片N含量、叶绿素含量(Chl)及非结构性碳水化合物(NSC)指标进行了测定。结果表明:1)在增温条件下,杉木幼树净光合速率(P_n)和水分利用效率(WUE)显著增加,分别增加了71.4%、51.3%,增温后杉木叶片能维持较高的气孔导度(G_s)、蒸腾速率(T_r)和胞间二氧化碳浓度(C_i)。2)增温促进土壤有机氮矿化作用,使土壤中可供植物吸收利用的有效N含量显著增加,从而引起杉木叶片N含量显著提高。而N作为叶绿素的重要组成物质,增温后,叶片N含量显著提高,最终导致杉木幼树叶片Chl a、Chl b及Chl总量显著增加,增加比例分别为76.3%、55.8%、68.7%,Chl a/b值亦呈增加趋势。3)增温对杉木幼树生长及叶片NSC含量并无显著影响。综上所述,增温通过改变杉木叶片气孔导度敏感性以及促进杉木叶片Chl含量合成,增加叶片对CO_2的吸收以及光能捕获能力,进而提高光合效率。同时,增温引起的根系高温可能大幅度提高杉木呼吸强度,加剧对杉木叶片碳水化合物的消耗过程,使其NSC含量无显著变化,从而导致杉木幼树生长无显著差异。     

不同林龄杉木人工林土壤团聚体磷素分布特征

探究不同林龄杉木人工林土壤团聚体各形态磷素的分布特征有利于提升杉木人工林土壤磷素有效性。本研究选取位于广西融水县的幼龄(9 a)、中龄(17 a)、成熟(26 a)杉木人工林和邻近撂荒地(CK),利用干筛法将采集到的表层(0～20 cm)原状土壤分为4个粒级团聚体(>2、1～2、0.25～1和<0.25 mm),测定各粒级团聚体中不同形态磷组分。结果表明: 1)不同林龄杉木人工林土壤团聚体组成差异显著,CK和各林龄杉木人工林中>2 mm粒级团聚体含量显著较高,随林龄的增长先增后减,在17 a时最高;土壤平均重量直径(MWD)和几何平均直径(GMD)的变化趋势与>2 mm粒级团聚体一致。2)CK和各林龄杉木人工林中各粒级土壤团聚体全磷、无机磷和有机磷含量差异均不显著,而土壤有效磷含量在>2 mm粒级团聚体中显著较高,达1.23～7.33 mg·kg^-1;不同林龄杉木人工林土壤团聚体及全土全磷、有效磷和无机磷含量均显著高于CK,并随杉木林龄的增长先增后减,全土总磷和有效磷含量在9 a时最高,分别为322.40和7.33 mg·kg^-1,全土无机磷含量在17 a时最高,为114.05 mg·kg^-1;全土有机磷含量随杉木林龄的增长先增再减再增,在9 a时最高,为210.00 mg·kg^-1。3)不同粒级土壤团聚体磷储量与土壤团聚体组成比例显著相关。CK和各林龄杉木人工林中>2 mm粒级团聚体各形态磷储量较高。除有机磷外,各形态土壤磷储量均随杉木林龄的增长先增后减。综上,林龄17 a之前,杉木人工林的种植有利于提升土壤团聚体稳定性,促进土壤磷素水平的提升;林龄17 a后,>2 mm粒级团聚体的破碎导致土壤团聚体稳定性和土壤磷素供应水平逐渐下降。因此,在杉木人工林培育栽种17 a以后应重视土壤中>2 mm粒级团聚体的保护,以保障土壤质量,维持土壤供磷水平。     

适合度的相对性与路径依赖的自然选择

自然选择理论认为生物个体或者种群在进化的过程中, 其基因或者性状、行为策略的选择一定是能够提高其适合度或者达到某个可期的“目标”。然而, 随着某个突变基因或者性状特征、行为策略在种群中扩散, 其期望收益将随着其在种群中分布的密度变化或环境改变而发生改变, 这就是适合度景观的悖论, 即静态的、固定可期望的收益可能因此而不存在。基于动态而非静态适合度景观的概念, 我们提出路径依赖的自然选择概念。路径依赖的自然选择过程中, 一个突变的基因或表型在某种环境下随机产生, 但是该基因或表型在某些特定环境下会产生正反馈。尤其是在正反馈与随机漂变的共同作用下, 多条路径的演化就可能发生, 并且其路径的形成将同时受到其种群进化历史过程和空间特征分布等因素的强烈影响。而在不同路径下, 由于观测维度、角度和尺度的不同, 适合度意义将因此而存在不同。在此意义下, 自然选择更可能选择路径频率而不是适合度大小。基于上述概念, 我们借鉴现代物理学中复函数的方法, 来描述多重动力对物种形成或者生物特征、种群进化等路径依赖的演化过程, 以期为同域物种、隐存种形成以及生物多样性演化提供解释机制。     

MALDI-TOF mass spectrometry rapid pathogen identification and outcomes of patients with bloodstream infection: A systematic review and meta-analysis

There was inconsistent evidence regarding the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for microorganism identification with/without antibiotic stewardship team (AST) and the clinical outcome of patients with bloodstream infections (BSI). In a systematic review and meta-analysis, we evaluated the effectiveness of rapid microbial identification by MALDI-TOF MS with and without AST on clinical outcomes. We searched PubMed and EMBASE databases from inception to 1 February 2022 to identify pre–post and parallel comparative studies that evaluated the use of MALDI-TOF MS for microorganism identification. Pooled effect estimates were derived using the random-effects model. Twenty-one studies with 14,515 patients were meta-analysed. Compared with conventional phenotypic methods, MALDI-TOF MS was associated with a 23% reduction in mortality (RR = 0.77; 95% CI: 0.66; 0.90; I² = 35.9%; 13 studies); 5.07-h reduction in time to effective antibiotic therapy (95% CI: −5.83; −4.31; I² = 95.7%); 22.86-h reduction in time to identify microorganisms (95% CI: −23.99; −21.74; I² = 91.6%); 0.73-day reduction in hospital stay (95% CI: −1.30; −0.16; I² = 53.1%); and US$4140 saving in direct hospitalization cost (95% CI: $-8166.75; $-113.60; I² = 66.1%). No significant heterogeneity sources were found, and no statistical evidence for publication bias was found. Rapid pathogen identification by MALDI-TOF MS with or without AST was associated with reduced mortality and improved outcomes of BSI, and may be cost-effective among patients with BSI.     

Lipid nanoparticle-encapsulated mRNA antibody provides long-term protection against SARS-CoV-2 in mice and hamsters

Monoclonal antibodies represent important weapons in our arsenal to against the COVID-19 pandemic. However, this potential is severely limited by the time-consuming process of developing effective antibodies and the relative high cost of manufacturing. Herein, we present a rapid and cost-effective lipid nanoparticle (LNP) encapsulated-mRNA platform for in vivo delivery of SARS-CoV-2 neutralization antibodies. Two mRNAs encoding the light and heavy chains of a potent SARS-CoV-2 neutralizing antibody HB27, which is currently being evaluated in clinical trials, were encapsulated into clinical grade LNP formulations (named as mRNA-HB27-LNP). In vivo characterization demonstrated that intravenous administration of mRNA-HB27-LNP in mice resulted in a longer circulating half-life compared with the original HB27 antibody in protein format. More importantly, a single prophylactic administration of mRNA-HB27-LNP provided protection against SARS-CoV-2 challenge in mice at 1, 7 and even 63 days post administration. In a close contact transmission model, prophylactic administration of mRNA-HB27-LNP prevented SARS-CoV-2 infection between hamsters in a dose-dependent manner. Overall, our results demonstrate a superior long-term protection against SARS-CoV-2 conferred by a single administration of this unique mRNA antibody, highlighting the potential of this universal platform for antibody-based disease prevention and therapy against COVID-19 as well as a variety of other infectious diseases.Subject terms: Biological techniques, Immunology